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Sample records for c-c motif receptor

  1. Inhibition of chemokine (C-C motif receptor 7 sialylation suppresses CCL19-stimulated proliferation, invasion and anti-anoikis.

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    Mei-Lin Su

    Full Text Available Chemokine (C-C motif receptor 7 (CCR7 is involved in lymph-node homing of naive and regulatory T cells and lymphatic metastasis of cancer cells. Sialic acids comprise a group of monosaccharide units that are added to the terminal position of the oligosaccharide chain of glycoproteins by sialyation. Recent studies suggest that aberrant sialylation of receptor proteins contributes to proliferation, motility, and drug resistance of cancer cells. In this study, we addressed whether CCR7 is a sialylated receptor protein and tried to elucidate the effect of sialylation in the regulation of signal transduction and biological function of CCR7. Our results demonstrated that α-2, 3-sialyltransferase which catalyze sialylation reaction in vivo was overexpressed in breast tumor tissues and cell lines. Lectin blot analysis clearly demonstrated that CCR7 receptor was sialyated in breast cancer cells. Chemokine (C-C motif ligand 19 (CCL19, the cognate ligand for CCR7, induced the activation of extracellular signal-regulated kinase (ERK and AKT signaling and increased the expression of cell cycle regulatory proteins and proliferation of breast cancer cells. When cells were pre-treated with a sialyltransferase inhibitor AL10 or sialidase, CCL19-induced cell growth was significantly suppressed. CCL19 also increased invasion and prevented anoikis by up-regulating pro-survival proteins Bcl-2 and Bcl-xL. Inhibition of sialylation by AL10 totally abolished these effects. Finally, we showed that AL10 inhibited tumorigenicity of breast cancer in experimental animals. Taken together, we demonstrate for the first time that CCR7 receptor is a sialylated protein and sialylation is important for the paracrine stimulation by its endogenous ligand CCL19. In addition, inhibition of aberrant sialylation of CCR7 suppresses proliferation and invasion and triggers anoikis in breast cancer cells. Targeting of sialylation enzymes may be a novel strategy for breast cancer treatment.

  2. The Role of C-C Motif Chemokine Receptor-2 in Human Vein Endothelial Cells Migration%CC类趋化因子受体2在人内皮细胞迁移中的作用

    Institute of Scientific and Technical Information of China (English)

    赵宁; 赵俐杰

    2016-01-01

    目的:探讨CC类趋化因子受体2(CCR2)对人脐静脉血管内皮细胞(HUVECs)迁移的作用。方法 RT-PCR和Western-blot检测单核细胞趋化蛋白-1(MCP1)对HUVECs CCR2蛋白表达的影响。 Transwell实验观察CCR2拮抗剂对HUVECs迁移的影响。结果在 HUVECs中 CCR2蛋白表达存在 MCP1浓度依赖方式, Transwell 实验显示 CCR2拮抗剂(RS504393)抑制细胞迁移(P<0.01)。结论 CCR2对人内皮细胞迁移有促进作用,其作用与MCP1结合相关。%Objective To explore the effect of C-C motif chemokine receptor -2 ( CCR2 ) on the migration of human umbilical vein endothelial cells (HUVECs). Methods The effect of monocyte chemoattractant protein-1 (MCP1) on the expression of CCR2 in HUVECs was measured by RT-PCR and Western blot. The effect of anti-CCR2 polyclonal antibodies (RS504393) on the migration of HUVECs was measured by Transwell migration assay. Results CCR2 was dose-dependently induced by MCP1 in HUVECs. The migrating of cells was significantly inhibited by RS504393. Conclusion CCR2 can accelerate the migration of HUVECs, which may be associated with MCP-1 binding.

  3. Chemokine (C-C motif ligand 2 mediates direct and indirect fibrotic responses in human and murine cultured fibrocytes

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    Ekert Jason E

    2011-10-01

    Full Text Available Abstract Background Fibrocytes are a population of circulating bone-marrow-derived cells that express surface markers for leukocytes and mesenchymal cells, and are capable of differentiating into myofibroblasts. They have been observed at sites of active fibrosis and increased circulating numbers correlate with mortality in idiopathic pulmonary fibrosis (IPF. Inhibition of chemokine (C-C motif receptor 2 (CCR2 during experimental models of lung fibrosis reduces lung collagen deposition, as well as reducing lung fibrocyte accumulation. The aim of the present study was to determine whether human and mouse fibrocytes express functional CCR2. Results Following optimized and identical human and murine fibrocyte isolation, both cell sources were shown to be positive for CCR2 by flow cytometry and this expression colocalized with collagen I and CD45. Human blood fibrocytes stimulated with the CCR2 ligand chemokine (C-C motif ligand 2 (CCL2, demonstrated increased proliferation (P P P Conclusions This study directly compares the functional responses of human and murine fibrocytes to CCR2 ligands, and following comparable isolation techniques. We have shown comparable biological effects, strengthening the translatability of the murine models to human disease with respect to targeting the CCR2 axis to ameliorate disease in IPF patients.

  4. 趋化因子5及其受体CCR5与糖尿病并发症%Role of chemokine(c-c motif) ligand 5 and its receptor CCR5 in diabetic complication

    Institute of Scientific and Technical Information of China (English)

    李桂林; 梁尚栋

    2011-01-01

    Chemokines are a large family of small cytokines that control cell trafficking. Chemokines and their receptors are intimately involved in the process of inflammatory and inducibly expression. Therefore, the primal studies were confined to the immune system. However, recent intriguing findings reveal that chemokines are not only involved in the inflammatory process of diabetes, but also play the important regulative role in the genesis and development of diabetic complication. This review summarizes the recent advances in the role of chemokine ligand 5 ( CCL5 ) and its receptor chemokine receptor 5( CCR5 ) in diabetic complication and their mechanisms concerned, which will help further understand the relationship between chemokines and diabetes and will provide evidence for further research.%趋化因子是一组能够趋化细胞定向移动的小分子细胞因子,参与白细胞迁移的调控,在炎症中诱导性表达,与炎症过程密切相关,最初的研究主要局限于免疫系统.近几年来研究发现,趋化因子不仅参与糖尿病的炎症过程,而且在糖尿病并发症的发生发展中发挥重要的调节作用.该文主要针对趋化因子5及其受体CCR5在糖尿病并发症中的作用及相关机制的研究予以综述,以便深入理解趋化因子与糖尿病的关系,为进一步的研究提供帮助.

  5. Vascular Stem/Progenitor Cell Migration Induced by Smooth Muscle Cell-Derived Chemokine (C-C Motif) Ligand 2 and Chemokine (C-X-C motif) Ligand 1 Contributes to Neointima Formation.

    Science.gov (United States)

    Yu, Baoqi; Wong, Mei Mei; Potter, Claire M F; Simpson, Russell M L; Karamariti, Eirini; Zhang, Zhongyi; Zeng, Lingfang; Warren, Derek; Hu, Yanhua; Wang, Wen; Xu, Qingbo

    2016-09-01

    Recent studies have shown that Sca-1(+) (stem cell antigen-1) stem/progenitor cells within blood vessel walls may contribute to neointima formation, but the mechanism behind their recruitment has not been explored. In this work Sca-1(+) progenitor cells were cultivated from mouse vein graft tissue and found to exhibit increased migration when cocultured with smooth muscle cells (SMCs) or when treated with SMC-derived conditioned medium. This migration was associated with elevated levels of chemokines, CCL2 (chemokine (C-C motif) ligand 2) and CXCL1 (chemokine (C-X-C motif) ligand 1), and their corresponding receptors on Sca-1(+) progenitors, CCR2 (chemokine (C-C motif) receptor 2) and CXCR2 (chemokine (C-X-C motif) receptor 2), which were also upregulated following SMC conditioned medium treatment. Knockdown of either receptor in Sca-1(+) progenitors significantly inhibited cell migration. The GTPases Cdc42 and Rac1 were activated by both CCL2 and CXCL1 stimulation and p38 phosphorylation was increased. However, only Rac1 inhibition significantly reduced migration and p38 phosphorylation. After Sca-1(+) progenitors labeled with green fluorescent protein (GFP) were applied to the adventitial side of wire-injured mouse femoral arteries, a large proportion of GFP-Sca-1(+) -cells were observed in neointimal lesions, and a marked increase in neointimal lesion formation was seen 1 week post-operation. Interestingly, Sca-1(+) progenitor migration from the adventitia to the neointima was abrogated and neointima formation diminished in a wire injury model using CCL2(-/-) mice. These findings suggest vascular stem/progenitor cell migration from the adventitia to the neointima can be induced by SMC release of chemokines which act via CCR2/Rac1/p38 and CXCR2/Rac1/p38 signaling pathways. Stem Cells 2016;34:2368-2380.

  6. Chemokine (C-C motif ligand 20, a potential biomarker for Graves' disease, is regulated by osteopontin.

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    Xiaoli Li

    Full Text Available CONTEXT: Graves' disease (GD is a common autoimmune disease involving the thyroid gland. The altered balance of pro- and anti-inflammatory cytokines plays an important role in the pathogenesis of GD. Chemokine (C-C motif ligand 20 (CCL20 is important for interleukin-17 (IL-17 signal activation and a potent chemoattractant for Th17 cells. Meanwhile, Osteopontin (OPN, a broadly expressed pleiotropic cytokine, has been implicated in GD through inducing Th1-involved response to enhance the production of proinflammatory cytokines and chemokines, but little is known about the role of OPN in regulating CCL20 and IL-17 signaling. OBJECTIVE: This study sought to explore the possibility of CCL20 level as a biomarker for GD, as well as investigate the role of OPN in regulating CCL20 production. METHODS: Fifty untreated GD patients, fifteen euthyroid GD patients, twelve TRAb-negative GD patients and thirty-five healthy control donors were recruited. OPN, CCL20 and other clinical GD diagnosis parameters were measured. CD4+T cells were isolated from peripheral blood mononuclear cells (PBMCs using antibody-coated magnetic beads. Enzyme-linked immune-sorbent assay and quantitative polymerase chain reaction were used to determine CCL20 expression level. RESULTS: We found that the plasma CCL20 level was enhanced in GD patients and decreased in euthyroid and TRAb-negative GD patients. In addition, CCL20 level correlated with GD clinical diagnostic parameters and plasma OPN level. Moreover, we demonstrated that recombinant OPN and plasma from untreated GD patients increased the expression of CCL20 in CD4+T cells, which could be blocked by OPN antibody. Furthermore, we found that the effect of OPN on CCL20 expression was mediated by β3 integrin receptor, IL-17, NF-κB and MAPK pathways. CONCLUSIONS: These results demonstrated that CCL20 might serve as a biomarker for GD and suggested the possible role of OPN in induction of CCL20 expression.

  7. Chemokine signaling involving chemokine (C-C motif) ligand 2 plays a role in descending pain facilitation

    Institute of Scientific and Technical Information of China (English)

    Wei Guo; Hu Wang; Shiping Zou; Ronald Dubner; Ke Ren

    2012-01-01

    Objective Despite accumulating evidence on a role of immune cells and their associated chemicals in mechanisms of pain,few studies have addressed the potential role of chemokines in the descending facilitation of persistent pain.The present study was undertaken to test the hypothesis that the chemokine (C-C motif) ligand 2 (CCL2) (commonly known as monocyte chemoattractant protein-1) signaling in the rostral ventromedial medulla (RVM),a pivotal structure in brainstem pain modulatory circuitry,is involved in descending pain facilitation in rats.Methods An L5 spinal nerve ligation (SNL) was produced in rats under pentobarbital anesthesia.Western blot and immunohistochemistry were used to detect the expression levels of CCL2 and CCL2 receptor (CCR2),and examine their distributions compared with the neuronal marker NeuN as well as glial markers glial fibrillary acidic protein (GFAP,astroglial) and CD11b (microglial),respectively.Results SNL induced an increase in CCL2 expression in the RVM,and this returned to the control level at 4 weeks after injury.The induced CCL2 colocalized with NeuN,but not with GFAP and CD11b.CCR2 was also upregulated by SNL in the RVM,and this increase lasted for at least 4 weeks.CCR2 was colocalized with CD1 1b but not GFAP.Few RVM neurons also exhibited CCR2 staining.Neutralizing CCL2 with an anti-CCL2 antibody (0.2-20 ng) or injecting RS-102895 (0.1-10 pmol),a CCR2b chemokine receptor antagonist,into the RVM on day 1 after SNL,significantly attenuated the established thermal and mechanical hypersensitivity.In addition,injection of recombinant rat CCL2 (0.03-3pmol) into the RVM induced dose-dependent hyperalgesia,which was prevented by pretreatment with RS-102895 (10pmol).Interleukin-1β (IL-1β),a potent inducer of neuronal CCL2,was also selectively upregulated in RVM reactive astrocytes.Injection of IL-1β (120 fmol) into the RVM induced behavioral hyperalgesia,which was blocked by RS-102895(10 pmol).However,an IL-1 receptor antagonist (3

  8. Chemokine (C-C motif) Ligand 2 is a potential biomarker of inflammation & physical fitness in obese children: a cross-sectional study

    OpenAIRE

    Samaan, M Constantine; Obeid, Joyce; Nguyen, Thanh,; Thabane, Lehana; Timmons, Brian W

    2013-01-01

    Background Obesity is a global epidemic that is impacting children around the world. Obesity is a chronic inflammatory state with enhanced production of multiple cytokines and chemokines. Chemokine (C-C motif) Ligand 2 (CCL2) is produced by immune and metabolic cells and attracts immune cells into liver, muscle and adipose tissue, resulting in initiation and propagation of the inflammatory response in obesity. How obesity and fitness affect the production of this chemokine in children is unkn...

  9. Distinct recognition modes of FXXLF and LXXLL motifs by the androgen receptor.

    NARCIS (Netherlands)

    H.J. Dubbink (Erik Jan); R. Hersmus (Remko); C.S. Verma (Chandra); H.A.G.M. van der Korput (Hetty); C.A. Berrevoets (Cor); J. van Tol (Judith); A.C.J. Ziel-van der Made (Angelique); A.O. Brinkmann (Albert); A.C. Pike (Ashley); J. Trapman (Jan)

    2004-01-01

    textabstractAmong nuclear receptors, the androgen receptor (AR) is unique in that its ligand-binding domain (LBD) interacts with the FXXLF motif in the N-terminal domain, resembling coactivator LXXLL motifs. We compared AR- and estrogen receptor alpha-LBD interactions of the wild-t

  10. Changes in plasma chemokine C-C motif ligand 2 levels during treatment with eicosapentaenoic acid predict outcome in patients undergoing surgery for colorectal cancer liver metastasis

    Science.gov (United States)

    Volpato, Milene; Perry, Sarah L; Marston, Gemma; Ingram, Nicola; Cockbain, Andrew J.; Burghel, Heather; Jake, Mann; Lowes, David; Wilson, Erica; Droop, Alastair; Randerson-Moor, Juliette; Coletta, P Louise; Hull, Mark A

    2016-01-01

    The mechanism of the anti-colorectal cancer (CRC) activity of the omega-3 fatty acid eicosapentaenoic acid (EPA) is not understood. We tested the hypothesis that EPA reduces expression of chemokine C-C motif ligand 2 (CCL2), a pro-inflammatory chemokine with known roles in metastasis. We measured CCL2 in clinical samples from a randomized trial of EPA in patients undergoing liver surgery for CRC liver metastasis (LM) and preclinical models. Genome-wide transcriptional profiling of tumors from EPA-treated patients was performed. EPA decreased CCL2 synthesis by CRC cells in a dose-dependent manner. CCL2 was localized to malignant epithelial cells in human CRCLM. EPA did not reduce CCL2 content in human or mouse tumors compare to control. However, EPA treatment was associated with decreased plasma CCL2 levels compared with controls (P=0.04). Reduction in plasma CCL2 following EPA treatment predicted improved disease-free survival (HR 0.32; P=0.003). Lack of ‘CCL2 response’ was associated with a specific CRCLM gene expression signature. In conclusion, reduction in plasma CCL2 in patients with CRCLM treated with EPA predicts better clinical outcome and a specific tumor gene expression profile. Further work is needed to validate CCL2 as a therapeutic response biomarker for omega-3 fatty acid treatment of CRC patients. PMID:27058904

  11. C-C chemokine receptor-7 mediated endocytosis of antibody cargoes into intact cells

    Directory of Open Access Journals (Sweden)

    Xavier eCharest-Morin

    2013-09-01

    Full Text Available The C-C chemokine receptor-7 (CCR7 is a G protein coupled receptor that has a role in leukocyte homing, but that is also expressed in aggressive tumor cells. Preclinical research supports that CCR7 is a valid target in oncology. In view of the increasing availability of therapeutic monoclonal antibodies that carry cytotoxic cargoes, we studied the feasibility of forcing intact cells to internalize known monoclonal antibodies by exploiting the cycle of endocytosis and recycling triggered by the CCR7 agonist CCL19. Firstly, an anti-CCR7 antibody (CD197; clone 150503 labeled surface recombinant CCR7 expressed in intact HEK 293a cells and the fluorescent antibody was internalized following CCL19 treatment. Secondly, a recombinant myc-tagged CCL19 construction was exploited along the anti-myc monoclonal antibody 4A6. The myc-tagged ligand was produced as a conditioned medium of transfected HEK 293a cells that contained the equivalent of 430 ng/ml of immunoreactive CCL19 (average value, ELISA determination. CCL19-myc, but not authentic CCL19, carried the fluorophore-labeled antibody 4A6 into other recipient cells that expressed recombinant CCR7 (microscopy, cytofluorometry. The immune complexes were apparent in endosomal structures, colocalized well with the small GTPase Rab5 and progressed toward Rab7-positive endosomes. A dominant negative form of Rab5 (GDP-locked inhibited this endocytosis. Further, endosomes in CCL19-myc- or CCL19-stimulated cells were positive for β-arrestin2, but rarely for β-arrestin1. Following treatment with CCL19-myc and the 4A6 antibody, the melanoma cell line A375 that expresses endogenous CCR7 was specifically stained using a secondary peroxidase-conjugated antibody. Agonist-stimulated CCR7 can transport antibody-based cargoes, with possible therapeutic applications in oncology.

  12. Human C-C chemokine receptor 3 monoclonal antibody inhibits pulmonary inflammation in allergic mice

    Institute of Scientific and Technical Information of China (English)

    Kai WANG; Hua-hao SHEN; Wen LI; Hua-qiong HUANG

    2007-01-01

    Aim:To evaluate the effect of C-C chemokine receptor 3 (CCR3) blockade on pulmonary inflammation and mucus production in allergic mice. Methods:We used the synthetic peptide of the CCR3 NH2-terminal as the immunizing antigen and generated murine monoclonal antibody against the human CCR3. In addition,the generated antibody was administered to mice sensitized and challenged with ovalbumin. The inflammatory cells in bronchoalveolar lavage,cytokine levels,pulmonary histopathology,and mucus secretion were examined. Results:The Western blotting analysis indicated that the generated antibody bound to CCR3 specifically. The allergic mice treated with the antihuman CCR3 antibody exhibited a significant reduction of pulmonary inflammation accompanied with the alteration of cytokine. Conclusion:The antibody we generated was specific to CCR3. The inhibition of airway inflammation and mucus overproduction by the antibody suggested that the blockade of CCR3 is an appealing therapeutical target for asthma. The present research may provide an experimental basis for the further study of this agent.

  13. Lead Screening for HIV of C-C Chemokine Receptor Type 5 Receptor Inhibited by Traditional Chinese Medicine

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    Tzu-Chieh Hung

    2014-01-01

    Full Text Available The acquired immunodeficiency syndrome (AIDS, caused by the human immunodeficiency virus (HIV, has become a serious world-wide problem because of this disease's rapid propagation and incurability. Recent research has pointed out that the C-C chemokine receptor type 5 (CCR5 is an important target for HIV infection. The traditional Chinese medicine (TCM database (http://tcm.cmu.edu.tw/ has been screened for molecular compounds that, by simulating molecular docking and molecular dynamics, may protect CCR5 against HIV. Saussureamine C, 5-hydroxy-L-tryptophan, and abrine are selected based on the docking score being higher than Maraviroc and other TCM compounds. The molecular dynamics are helpful in the analysis and detection of protein-ligand interactions. According to the docking poses, hydrophobic interactions, and hydrogen bond variations, this research surmises TRP86, TYR108, GLN194, TYR251, and GLU283 are the main regions of important amino acids in CCR5. In addition to the detection of TCM compound efficacy, we suggest saussureamine C is better than the others for maintaining protein composition during protein-ligand interaction, based on the structural variation.

  14. Coregulator control of androgen receptor action by a novel nuclear receptor-binding motif.

    Science.gov (United States)

    Jehle, Katja; Cato, Laura; Neeb, Antje; Muhle-Goll, Claudia; Jung, Nicole; Smith, Emmanuel W; Buzon, Victor; Carbó, Laia R; Estébanez-Perpiñá, Eva; Schmitz, Katja; Fruk, Ljiljana; Luy, Burkhard; Chen, Yu; Cox, Marc B; Bräse, Stefan; Brown, Myles; Cato, Andrew C B

    2014-03-28

    The androgen receptor (AR) is a ligand-activated transcription factor that is essential for prostate cancer development. It is activated by androgens through its ligand-binding domain (LBD), which consists predominantly of 11 α-helices. Upon ligand binding, the last helix is reorganized to an agonist conformation termed activator function-2 (AF-2) for coactivator binding. Several coactivators bind to the AF-2 pocket through conserved LXXLL or FXXLF sequences to enhance the activity of the receptor. Recently, a small compound-binding surface adjacent to AF-2 has been identified as an allosteric modulator of the AF-2 activity and is termed binding function-3 (BF-3). However, the role of BF-3 in vivo is currently unknown, and little is understood about what proteins can bind to it. Here we demonstrate that a duplicated GARRPR motif at the N terminus of the cochaperone Bag-1L functions through the BF-3 pocket. These findings are supported by the fact that a selective BF-3 inhibitor or mutations within the BF-3 pocket abolish the interaction between the GARRPR motif(s) and the BF-3. Conversely, amino acid exchanges in the two GARRPR motifs of Bag-1L can impair the interaction between Bag-1L and AR without altering the ability of Bag-1L to bind to chromatin. Furthermore, the mutant Bag-1L increases androgen-dependent activation of a subset of AR targets in a genome-wide transcriptome analysis, demonstrating a repressive function of the GARRPR/BF-3 interaction. We have therefore identified GARRPR as a novel BF-3 regulatory sequence important for fine-tuning the activity of the AR.

  15. CXC motif chemokine receptor 4 gene polymorphism and cancer risk

    Science.gov (United States)

    Wu, Yang; Zhang, Chun; Xu, Weizhang; Zhang, Jianzhong; Zheng, Yuxiao; Lu, Zipeng; Liu, Dongfang; Jiang, Kuirong

    2016-01-01

    Abstract Background: Previous epidemiological studies have reported the relationship between CXC motif chemokine receptor 4 (CXCR4) synonymous polymorphism (rs2228014), and risk of cancer, but the results remained conflicting and controversial. Therefore, this study was devised to evaluate the genetic effects of the rs2228014 polymorphism on cancer risk in a large meta-analysis. Methods: The computer-based databases (EMBASE, Web of Science, and PubMed) were searched for all relevant studies evaluating rs2228014 and susceptibility to cancer. In the analysis, pooled odds ratios (ORs) with its corresponding 95% confidence intervals (CIs) were calculated in 5 genetic models to assess the genetic risk. Egger regression and Begg funnel plots test were conducted to appraise the publication bias. Results: Data on rs2228014 polymorphism and overall cancer risk were available for 3684 cancer patients and 5114 healthy controls participating in 11 studies. Overall, a significantly increased risk of cancer was associated with rs2228014 polymorphism in homozygote model (OR = 2.01, 95% CI: 1.22–3.33) and in recessive model (OR = 1.97, 95% CI: 1.23–3.16). When stratified by ethnicity, the results were positive only in Asian populations (heterozygote model: OR = 1.36, 95% CI: 1.13–1.65; homozygote model: OR = 2.43, 95% CI: 1.21–4.91; dominant model: OR = 1.47, 95% CI: 1.13–1.90; recessive model: OR = 2.25, 95% CI: 1.13–4.48; and allele model: OR = 1.48, 95% CI: 1.10–1.99). Besides, in the subgroup analysis by source of control, the result was significant only in population-based control (homozygote model: OR = 2.39, 95% CI: 1.06–5.40; recessive model: pooled OR = 2.24, 95% CI: 1.02–4.96). Conclusion: In general, our results first indicated that the rs2228014 polymorphism in CXCR4 gene is correlated with an increased risk of cancer, especially among Asian ethnicity. Large, well-designed epidemiological studies are required to verify the current findings. PMID

  16. Multiple motifs regulate the trafficking of GABA(B) receptors at distinct checkpoints within the secretory pathway.

    Science.gov (United States)

    Restituito, Sophie; Couve, Andrés; Bawagan, Hinayana; Jourdain, Sabine; Pangalos, Menelas N; Calver, Andrew R; Freeman, Katie B; Moss, Stephen J

    2005-04-01

    gamma-Aminobutyric acid type B receptors (GABA(B)) are G-protein-coupled receptors that mediate GABAergic inhibition in the brain. Their functional expression is dependent upon the formation of heterodimers between GABA(B)R1 and GABA(B)R2 subunits, a process that occurs within the endoplasmic reticulum (ER). However, the mechanisms that regulate receptor surface expression remain largely unknown. Here, we demonstrate that access to the cell surface for GABA(B)R1 is sequentially controlled by an RSR(R) motif and a LL motif within its cytoplasmic domain. In addition, we reveal that msec7-1, a guanine-nucleotide-exchange factor (GEF) for the ADP-ribosylation factor (ARF) family of GTPases, critical regulators of vesicular membrane trafficking, interacts with GABA(B)R1 via the LL motif in this subunit. Finally, we establish that msec7-1 modulates the cell surface expression of GABA(B) receptors, a process that is dependent upon the integrity of the LL motif in GABA(B)R1. Together, our results demonstrate that the cell surface expression of the GABA(B)R1 subunit is regulated by multiple motifs, which act at distinct checkpoints in the secretory pathway, and also suggest a novel role for msec7-1 in regulating the membrane trafficking of GABA(B)R1 subunits.

  17. Structural Diversity in Conserved Regions Like the DRY-Motif among Viral 7TM Receptors-A Consequence of Evolutionary Pressure?

    DEFF Research Database (Denmark)

    Mølleskov-Jensen, Ann-Sofie; Sparre-Ulrich, Alexander Hovard; Davis-Poynter, Nicholas

    2012-01-01

    and the C-terminal tail. In the DRY-motif, the arginine residue serves important purposes by being directly involved in G protein coupling. Interestingly, among the viral receptors there is a greater diversity in the DRY-motif compared to their endogenous receptor homologous. The C-terminal receptor tail......Several herpes- and poxviruses have captured chemokine receptors from their hosts and modified these to their own benefit. The human and viral chemokine receptors belong to class A 7 transmembrane (TM) receptors which are characterized by several structural motifs like the DRY-motif in TM3...... motifs and discuss their role in viral 7TM receptor signaling compared to their endogenous counterparts....

  18. Novel DNA motif binding activity observed in vivo with an estrogen receptor α mutant mouse.

    Science.gov (United States)

    Hewitt, Sylvia C; Li, Leping; Grimm, Sara A; Winuthayanon, Wipawee; Hamilton, Katherine J; Pockette, Brianna; Rubel, Cory A; Pedersen, Lars C; Fargo, David; Lanz, Rainer B; DeMayo, Francesco J; Schütz, Günther; Korach, Kenneth S

    2014-06-01

    Estrogen receptor α (ERα) interacts with DNA directly or indirectly via other transcription factors, referred to as "tethering." Evidence for tethering is based on in vitro studies and a widely used "KIKO" mouse model containing mutations that prevent direct estrogen response element DNA- binding. KIKO mice are infertile, due in part to the inability of estradiol (E2) to induce uterine epithelial proliferation. To elucidate the molecular events that prevent KIKO uterine growth, regulation of the pro-proliferative E2 target gene Klf4 and of Klf15, a progesterone (P4) target gene that opposes the pro-proliferative activity of KLF4, was evaluated. Klf4 induction was impaired in KIKO uteri; however, Klf15 was induced by E2 rather than by P4. Whole uterine chromatin immunoprecipitation-sequencing revealed enrichment of KIKO ERα binding to hormone response elements (HREs) motifs. KIKO binding to HRE motifs was verified using reporter gene and DNA-binding assays. Because the KIKO ERα has HRE DNA-binding activity, we evaluated the "EAAE" ERα, which has more severe DNA-binding domain mutations, and demonstrated a lack of estrogen response element or HRE reporter gene induction or DNA-binding. The EAAE mouse has an ERα null-like phenotype, with impaired uterine growth and transcriptional activity. Our findings demonstrate that the KIKO mouse model, which has been used by numerous investigators, cannot be used to establish biological functions for ERα tethering, because KIKO ERα effectively stimulates transcription using HRE motifs. The EAAE-ERα DNA-binding domain mutant mouse demonstrates that ERα DNA-binding is crucial for biological and transcriptional processes in reproductive tissues and that ERα tethering may not contribute to estrogen responsiveness in vivo.

  19. Identification of HI-like loop in CELO adenovirus fiber for incorporation of receptor binding motifs.

    Science.gov (United States)

    Logunov, Denis Y; Zubkova, Olga V; Karyagina-Zhulina, Anna S; Shuvalova, Eugenia A; Karpov, Andrei P; Shmarov, Maxim M; Tutykhina, Irina L; Alyapkina, Yulia S; Grezina, Natalia M; Zinovieva, Natalia A; Ernst, Lev K; Gintsburg, Alexsandr L; Naroditsky, Boris S

    2007-09-01

    Vectors based on the chicken embryo lethal orphan (CELO) avian adenovirus (Ad) have two attractive properties for gene transfer applications: resistance to preformed immune responses to human Ads and the ability to grow in chicken embryos, allowing low-cost production of recombinant viruses. However, a major limitation of this technology is that CELO vectors demonstrate decreased efficiency of gene transfer into cells expressing low levels of the coxsackie-Ad receptor (CAR). In order to improve the efficacy of gene transfer into CAR-deficient cells, we modified viral tropism via genetic alteration of the CELO fiber 1 protein. The alphav integrin-binding motif (RGD) was incorporated at two different sites of the fiber 1 knob domain, within an HI-like loop that we identified and at the C terminus. Recombinant fiber-modified CELO viruses were constructed containing secreted alkaline phosphatase (SEAP) and enhanced green fluorescent protein genes as reporter genes. Our data show that insertion of the RGD motif within the HI-like loop of the fiber resulted in significant enhancement of gene transfer into CAR-negative and CAR-deficient cells. In contrast, CELO vectors containing the RGD motif at the fiber 1 C terminus showed reduced transduction of all cell lines. CELO viruses modified with RGD at the HI-like loop transduced the SEAP reporter gene into rabbit mammary gland cells in vivo with an efficiency significantly greater than that of unmodified CELO vector and similar to that of Ad type 5 vector. These results illustrate the potential for efficient CELO-mediated gene transfer into a broad range of cell types through modification of the identified HI-like loop of the fiber 1 protein.

  20. Analogs of LDL Receptor Ligand Motifs in Dengue Envelope and Capsid Proteins as Potential Codes for Cell Entry

    OpenAIRE

    Juan Guevara; Jaime Romo; Troy McWhorter; Natalia Valentinova Guevara

    2015-01-01

    It is established that cell entry of low density lipoprotein particles (LLPs) containing Apo B100 and Apo E is mediated by receptors and GAGs. Receptor ligand motifs, XBBBXXBX, XBBXBX, and ΨBΨXB, and mono- and bipartite NLS sequences are abundant in Apo E and Apo B100 as well as in envelope and capsid proteins of Dengue viruses 1–4 (DENV1–4). Synthetic, fluorescence-labeled peptides of sequences in DENV2 envelope protein, and DENV3 capsid that include these motifs were used to conduct a quali...

  1. Characterization of high affinity binding motifs for the discoidin domain receptor DDR2 in collagen.

    Science.gov (United States)

    Konitsiotis, Antonios D; Raynal, Nicolas; Bihan, Dominique; Hohenester, Erhard; Farndale, Richard W; Leitinger, Birgit

    2008-03-14

    The discoidin domain receptors, DDR1 and DDR2, are receptor tyrosine kinases that are activated by native triple-helical collagen. Here we have located three specific DDR2 binding sites by screening the entire triple-helical domain of collagen II, using the Collagen II Toolkit, a set of overlapping triple-helical peptides. The peptide sequence that bound DDR2 with highest affinity interestingly contained the sequence for the high affinity binding site for von Willebrand factor in collagen III. Focusing on this sequence, we used a set of truncated and alanine-substituted peptides to characterize the sequence GVMGFO (O is hydroxyproline) as the minimal collagen sequence required for DDR2 binding. Based on a recent NMR analysis of the DDR2 collagen binding domain, we generated a model of the DDR2-collagen interaction that explains why a triple-helical conformation is required for binding. Triple-helical peptides comprising the DDR2 binding motif not only inhibited DDR2 binding to collagen II but also activated DDR2 transmembrane signaling. Thus, DDR2 activation may be effected by single triple-helices rather than fibrillar collagen.

  2. Leucine-based receptor sorting motifs are dependent on the spacing relative to the plasma membrane

    DEFF Research Database (Denmark)

    Geisler, C; Dietrich, J; Nielsen, B L;

    1998-01-01

    amino acid, is constitutively active. In this study, we have investigated how the spacing relative to the plasma membrane affects the function of both types of leucine-based motifs. For phosphorylation-dependent leucine-based motifs, a minimal spacing of 7 residues between the plasma membrane...... and the phospho-acceptor was required for phosphorylation and thereby activation of the motifs. For constitutively active leucine-based motifs, a minimal spacing of 6 residues between the plasma membrane and the acidic residue was required for optimal activity of the motifs. In addition, we found that the acidic...

  3. A common molecular motif characterizes extracellular allosteric enhancers of GPCR aminergic receptors and suggests enhancer mechanism of action.

    Science.gov (United States)

    Root-Bernstein, Robert; Dillon, Patrick F

    2014-01-01

    Several classes of compounds that have no intrinsic activity on aminergic systems nonetheless enhance the potency of aminergic receptor ligands three-fold or more while significantly increasing their duration of activity, preventing tachyphylaxis and reversing fade. Enhancer compounds include ascorbic acid, ethylenediaminetetraacetic acid, corticosteroids, opioid peptides, opiates and opiate antagonists. This paper provides the first review of aminergic enhancement, demonstrating that all enhancers have a common, inobvious molecular motif and work through a common mechanism that is manifested by three common characteristics. First, aminergic enhancers bind directly to the amines they enhance, suggesting that the common structural motif is reflected in common binding targets. Second, one common target is the first extracellular loop of aminergic receptors. Third, at least some enhancers are antiphosphodiesterases. These observations suggest that aminergic enhancers act on the extracellular surface of aminergic receptors to keep the receptor in its high affinity state, trapping the ligand inside the receptor. Enhancer binding produces allosteric modifications of the receptor structure that interfere with phosphorylation of the receptor, thereby inhibiting down-regulation of the receptor. The mechanism explains how enhancers potentiate aminergic activity and increase duration of activity and makes testable predictions about additional compounds that should act as aminergic enhancers.

  4. HIV-1 Nef down-modulates C-C and C-X-C chemokine receptors via ubiquitin and ubiquitin-independent mechanism.

    Directory of Open Access Journals (Sweden)

    Prabha Chandrasekaran

    Full Text Available Human and Simian Immunodeficiency virus (HIV-1, HIV-2, and SIV encode an accessory protein, Nef, which is a pathogenesis and virulence factor. Nef is a multivalent adapter that dysregulates the trafficking of many immune cell receptors, including chemokine receptors (CKRs. Physiological endocytic itinerary of agonist occupied CXCR4 involves ubiquitinylation of the phosphorylated receptor at three critical lysine residues and dynamin-dependent trafficking through the ESCRT pathway into lysosomes for degradation. Likewise, Nef induced CXCR4 degradation was critically dependent on the three lysines in the C-terminal -SSLKILSKGK- motif. Nef directly recruits the HECT domain E3 ligases AIP4 or NEDD4 to CXCR4 in the resting state. This mechanism was confirmed by ternary interactions of Nef, CXCR4 and AIP4 or NEDD4; by reversal of Nef effect by expression of catalytically inactive AIP4-C830A mutant; and siRNA knockdown of AIP4, NEDD4 or some ESCRT-0 adapters. However, ubiquitinylation dependent lysosomal degradation was not the only mechanism by which Nef downregulated CKRs. Agonist and Nef mediated CXCR2 (and CXCR1 degradation was ubiquitinylation independent. Nef also profoundly downregulated the naturally truncated CXCR4 associated with WHIM syndrome and engineered variants of CXCR4 that resist CXCL12 induced internalization via an ubiquitinylation independent mechanism.

  5. Putative bioactive motif of tritrpticin revealed by an antibody with biological receptor-like properties.

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    Raghava Sharma

    Full Text Available Antimicrobial peptides represent one of the most promising future strategies for combating infections and microbial drug resistance. Tritrpticin is a 13mer tryptophan-rich cationic antimicrobial peptide with a broad spectrum of activity whose application in antimicrobial therapy has been hampered by ambiguity about its biological target and consequently the molecular interactions necessary for its antimicrobial activity. The present study provides clues about the mechanism of action of tritripticin by using a unique monoclonal antibody (mAb as a 'physiological' structural scaffold. A pool of mAbs were generated against tritrpticin and based on its high affinity and ability to bind tritrpticin analogs, mAb 6C6D7 was selected and characterized further. In a screening of phage displayed random peptides, this antibody was able to identify a novel antimicrobial peptide with low sequence homology to tritrpticin, suggesting that the mAb possessed the physico-chemical characteristics mimicking the natural receptor. Subsequently, thermodynamics and molecular modeling identified a core group of hydrophobic residues in tritrpticin arranged in a distorted's' shaped conformation as critical for antibody binding. Comparison of the mAb induced conformation with the micelle bound structure of tritrpticin reveals how a common motif may be able to interact with multiple classes of biomolecules thus extending the target range of this innate immune peptide. Based on the concurrence between thermodynamic and structural data our results reveal a template that can be used to design novel antimicrobial pharmacophores while simultaneously demonstrating at a more fundamental level the potential of mAbs to act as receptor surrogates.

  6. Preparation of specific polyclonal antibodies to a C-C chemokine receptor, CCR1, and determination of CCR1 expression on various types of leukocytes.

    Science.gov (United States)

    Su, S B; Mukaida, N; Wang, J; Nomura, H; Matsushima, K

    1996-11-01

    cDNA cloning has revealed the presence of at least three distinct human receptors for macrophage inflammatory protein-1alpha (MIP-1alpha) and RANTES: C-C chemokine receptor (CCR) 1, 4, and 5. To clarify the physiological role of CCR1, we prepared specific antibodies to CCR1 by immunizing rabbits with recombinant glutathione-S-transferase (GST) fused with its NH2-terminal portion. The resultant antibodies stained positively 293 cells transfected with CCR1 cDNA but neither parental cells nor cells transfected with CXCR1 [interleukin-8 (IL-8) receptor type A] cDNA, confirming its specificity. Immunofluorescence analysis revealed that peripheral blood lymphocytes and monocytes but not neutrophils express CCR1. Positive staining of transfectants, monocytes, and lymphocytes was inhibited by the GST protein fused with the NH2-terminal portion of CCR1, further indicating that this antibody recognized the NH2-terminal portion of CC CKR1. A majority of CD3+, CD4+, CD8+, or CD16+ peripheral blood lymphocytes but not CD19+ lymphocytes expressed CCR1. Among CD4+ peripheral blood lymphocytes, CD45RO+ cells expressed a larger number of CCR1 compared with CD45RO-. Moreover, CD34+ cells in human bone marrow as well as cord blood were uniformly stained with this antibody. Furthermore, the antibody inhibited calcium mobilization in CCR1 transfectants stimulated with human rMIP-1alpha, suggesting that its NH2-terminal portion is critically involved in ligand binding or signaling. Finally, the antibody partially inhibited monocyte chemotactic activities of human rMIP-1alpha, suggesting that CCR1 is a functional receptor for MIP-1alpha on human peripheral blood monocytes.

  7. Comparative analysis of evolutionarily conserved motifs of epidermal growth factor receptor 2 (HER2 predicts novel potential therapeutic epitopes.

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    Xiaohong Deng

    Full Text Available Overexpression of human epidermal growth factor receptor 2 (HER2 is associated with tumor aggressiveness and poor prognosis in breast cancer. With the availability of therapeutic antibodies against HER2, great strides have been made in the clinical management of HER2 overexpressing breast cancer. However, de novo and acquired resistance to these antibodies presents a serious limitation to successful HER2 targeting treatment. The identification of novel epitopes of HER2 that can be used for functional/region-specific blockade could represent a central step in the development of new clinically relevant anti-HER2 antibodies. In the present study, we present a novel computational approach as an auxiliary tool for identification of novel HER2 epitopes. We hypothesized that the structurally and linearly evolutionarily conserved motifs of the extracellular domain of HER2 (ECD HER2 contain potential druggable epitopes/targets. We employed the PROSITE Scan to detect structurally conserved motifs and PRINTS to search for linearly conserved motifs of ECD HER2. We found that the epitopes recognized by trastuzumab and pertuzumab are located in the predicted conserved motifs of ECD HER2, supporting our initial hypothesis. Considering that structurally and linearly conserved motifs can provide functional specific configurations, we propose that by comparing the two types of conserved motifs, additional druggable epitopes/targets in the ECD HER2 protein can be identified, which can be further modified for potential therapeutic application. Thus, this novel computational process for predicting or searching for potential epitopes or key target sites may contribute to epitope-based vaccine and function-selected drug design, especially when x-ray crystal structure protein data is not available.

  8. Tyrosine kinase BMX phosphorylates phosphotyrosine-primed motif mediating the activation of multiple receptor tyrosine kinases.

    Science.gov (United States)

    Chen, Sen; Jiang, Xinnong; Gewinner, Christina A; Asara, John M; Simon, Nicholas I; Cai, Changmeng; Cantley, Lewis C; Balk, Steven P

    2013-05-28

    The nonreceptor tyrosine kinase BMX (bone marrow tyrosine kinase gene on chromosome X) is abundant in various cell types and activated downstream of phosphatidylinositol-3 kinase (PI3K) and the kinase Src, but its substrates are unknown. Positional scanning peptide library screening revealed a marked preference for a priming phosphorylated tyrosine (pY) in the -1 position, indicating that BMX substrates may include multiple tyrosine kinases that are fully activated by pYpY sites in the kinase domain. BMX phosphorylated focal adhesion kinase (FAK) at Tyr⁵⁷⁷ subsequent to its Src-mediated phosphorylation at Tyr⁵⁷⁶. Loss of BMX by RNA interference or by genetic deletion in mouse embryonic fibroblasts (MEFs) markedly impaired FAK activity. Phosphorylation of the insulin receptor in the kinase domain at Tyr¹¹⁸⁹ and Tyr¹¹⁹⁰, as well as Tyr¹¹⁸⁵, and downstream phosphorylation of the kinase AKT at Thr³⁰⁸ were similarly impaired by BMX deficiency. However, insulin-induced phosphorylation of AKT at Ser⁴⁷³ was not impaired in Bmx knockout MEFs or liver tissue from Bmx knockout mice, which also showed increased insulin-stimulated glucose uptake, possibly because of decreased abundance of the phosphatase PHLPP (PH domain leucine-rich repeat protein phosphatase). Thus, by identifying the pYpY motif as a substrate for BMX, our findings suggest that BMX functions as a central regulator among multiple signaling pathways mediated by tyrosine kinases.

  9. Cis and trans regulatory mechanisms control AP2-mediated B cell receptor endocytosis via select tyrosine-based motifs.

    Directory of Open Access Journals (Sweden)

    Kathleen Busman-Sahay

    Full Text Available Following antigen recognition, B cell receptor (BCR-mediated endocytosis is the first step of antigen processing and presentation to CD4+ T cells, a crucial component of the initiation and control of the humoral immune response. Despite this, the molecular mechanism of BCR internalization is poorly understood. Recently, studies of activated B cell-like diffuse large B cell lymphoma (ABC DLBCL have shown that mutations within the BCR subunit CD79b leads to increased BCR surface expression, suggesting that CD79b may control BCR internalization. Adaptor protein 2 (AP2 is the major mediator of receptor endocytosis via clathrin-coated pits. The BCR contains five putative AP2-binding YxxØ motifs, including four that are present within two immunoreceptor tyrosine-based activation motifs (ITAMs. Using a combination of in vitro and in situ approaches, we establish that the sole mediator of AP2-dependent BCR internalization is the membrane proximal ITAM YxxØ motif in CD79b, which is a major target of mutation in ABC DLBCL. In addition, we establish that BCR internalization can be regulated at a minimum of two different levels: regulation of YxxØ AP2 binding in cis by downstream ITAM-embedded DCSM and QTAT regulatory elements and regulation in trans by the partner cytoplasmic domain of the CD79 heterodimer. Beyond establishing the basic rules governing BCR internalization, these results illustrate an underappreciated role for ITAM residues in controlling clathrin-dependent endocytosis and highlight the complex mechanisms that control the activity of AP2 binding motifs in this receptor system.

  10. C-C chemokine receptor 2 inhibitor ameliorates hepatic steatosis by improving ER stress and inflammation in a type 2 diabetic mouse model.

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    Hong-Min Kim

    Full Text Available Hepatic steatosis is the accumulation of excess fat in the liver. Recently, hepatic steatosis has become more important because it occurs in the patients with obesity, type 2 diabetes, and hyperlipidemia and is associated with endoplasmic reticulum (ER stress and insulin resistance. C-C chemokine receptor 2 (CCR2 inhibitor has been reported to improve inflammation and glucose intolerance in diabetes, but its mechanisms remained unknown in hepatic steatosis. We examined whether CCR2 inhibitor improves ER stress-induced hepatic steatosis in type 2 diabetic mice. In this study, db/db and db/m (n = 9 mice were fed CCR2 inhibitor (2 mg/kg/day for 9 weeks. In diabetic mice, CCR2 inhibitor decreased plasma and hepatic triglycerides levels and improved insulin sensitivity. Moreover, CCR2 inhibitor treatment decreased ER stress markers (e.g., BiP, ATF4, CHOP, and XBP-1 and inflammatory cytokines (e.g., TNFα, IL-6, and MCP-1 while increasing markers of mitochondrial biogenesis (e.g., PGC-1α, Tfam, and COX1 in the liver. We suggest that CCR2 inhibitor may ameliorate hepatic steatosis by reducing ER stress and inflammation in type 2 diabetes mellitus.

  11. High constitutive activity of a virus-encoded seven transmembrane receptor in the absence of the conserved DRY motif (Asp-Arg-Tyr) in transmembrane helix 3

    DEFF Research Database (Denmark)

    Rosenkilde, Mette M; Kledal, Thomas N; Schwartz, Thue W

    2005-01-01

    The highly conserved Arg in the so-called DRY motif (Asp-Arg-Tyr) at the intracellular end of transmembrane helix 3 is in general considered as an essential residue for G protein coupling in rhodopsin-like seven transmembrane (7TM) receptors. In the open reading frame 74 (ORF74) receptor encoded ...

  12. Binding site characterization of G protein-coupled receptor by alanine-scanning mutagenesis using molecular dynamics and binding free energy approach: application to C-C chemokine receptor-2 (CCR2).

    Science.gov (United States)

    Chavan, Swapnil; Pawar, Shirishkumar; Singh, Rajesh; Sobhia, M Elizabeth

    2012-05-01

    The C-C chemokine receptor 2 (CCR2) was proved as a multidrug target in many diseases like diabetes, inflammation and AIDS, but rational drug design on this target is still lagging behind as the information on the exact binding site and the crystal structure is not yet available. Therefore, for a successful structure-based drug design, an accurate receptor model in ligand-bound state is necessary. In this study, binding-site residues of CCR2 was determined using in silico alanine scanning mutagenesis and the interactions between TAK-779 and the developed homology model of CCR2. Molecular dynamic simulation and Molecular Mechanics-Generalized Born Solvent Area method was applied to calculate binding free energy difference between the template and mutated protein. Upon mutating 29 amino acids of template protein and comparison of binding free energy with wild type, six residues were identified as putative hot spots of CCR2.

  13. Deficiency of C-C chemokine receptor 5 suppresses tumor development via inactivation of NF-κB and upregulation of IL-1Ra in melanoma model.

    Directory of Open Access Journals (Sweden)

    Ju Kyoung Song

    Full Text Available To evaluate the relevance of C-C chemokine receptor type 5 (CCR5 expression and tumor development, we compared melanoma growth in CCR5 knockout (CCR5(-/- mice and wild type (CCR5(+/+ mice. CCR5(-/- mice showed reduced tumor volume, tumor weight, and increased survival rate when compared to CCR5(+/+ mice. We investigated the activation of NF-κB since it is an implicated transcription factor in the regulation of genes involving cell growth, apoptosis, and tumor growth. Significant inhibition of DNA binding activity of NF-κB, and translocation of p50 and p65 into the nucleus through the inhibition of phosphorylation of IκB was found in the melanoma tissues of CCR5(-/- mice compared to melanoma tissues of CCR5(+/+ mice. NF-κB target apoptotic protein expression, such as cleaved caspase-3, cleaved PARP, and Bax, was elevated, whereas the survival protein expression levels, such as Bcl-2, C-IAP1, was decreased in the melanoma tissues of CCR5(-/- mice. Interestingly, we found that the level of IL-1Ra, a tumor growth suppressive cytokine, was significantly elevated in tumor tissue and spleen of CCR5(-/- mice compared to the level in CCR5(+/+ mice. Moreover, infiltration of CD8(+ cytotoxic T cell and CD57(+ natural killer cells was significantly increased in melanoma tumor and spleen tissue of CCR5(-/- mice compared to that of CCR5(+/+ mice. Therefore, these results showed that CCR5 deficiency caused apoptotic cell death of melanoma through inhibition of NF-κB and upregulation of IL-1Ra.

  14. Molecular characterization of the di-leucine-based internalization motif of the T cell receptor

    DEFF Research Database (Denmark)

    Dietrich, J; Hou, X; Wegener, A M;

    1996-01-01

    Several cell surface receptors including the T cell receptor (TCR) are phosphorylated and down-regulated following activation of protein kinases. We have recently shown that both phosphorylation of Ser-126 and the presence of the di-leucine sequence Leu-131 and Leu-132 in CD3 gamma are required f...

  15. Evidence of positive selection at codon sites localized in extracellular domains of mammalian CC motif chemokine receptor proteins

    Directory of Open Access Journals (Sweden)

    Metzger Kelsey J

    2010-05-01

    Full Text Available Abstract Background CC chemokine receptor proteins (CCR1 through CCR10 are seven-transmembrane G-protein coupled receptors whose signaling pathways are known for their important roles coordinating immune system responses through targeted trafficking of white blood cells. In addition, some of these receptors have been identified as fusion proteins for viral pathogens: for example, HIV-1 strains utilize CCR5, CCR2 and CCR3 proteins to obtain cellular entry in humans. The extracellular domains of these receptor proteins are involved in ligand-binding specificity as well as pathogen recognition interactions. In mammals, the majority of chemokine receptor genes are clustered together; in humans, seven of the ten genes are clustered in the 3p21-24 chromosome region. Gene conversion events, or exchange of DNA sequence between genes, have been reported in chemokine receptor paralogs in various mammalian lineages, especially between the cytogenetically closely located pairs CCR2/5 and CCR1/3. Datasets of mammalian orthologs for each gene were analyzed separately to minimize the potential confounding impact of analyzing highly similar sequences resulting from gene conversion events. Molecular evolution approaches and the software package Phylogenetic Analyses by Maximum Likelihood (PAML were utilized to investigate the signature of selection that has acted on the mammalian CC chemokine receptor (CCR gene family. The results of neutral vs. adaptive evolution (positive selection hypothesis testing using Site Models are reported. In general, positive selection is defined by a ratio of nonsynonymous/synonymous nucleotide changes (dN/dS, or ω >1. Results Of the ten mammalian CC motif chemokine receptor sequence datasets analyzed, only CCR2 and CCR3 contain amino acid codon sites that exhibit evidence of positive selection using site based hypothesis testing in PAML. Nineteen of the twenty codon sites putatively indentified as likely to be under positive

  16. The Medicago truncatula lysin [corrected] motif-receptor-like kinase gene family includes NFP and new nodule-expressed genes.

    Science.gov (United States)

    Arrighi, Jean-François; Barre, Annick; Ben Amor, Besma; Bersoult, Anne; Soriano, Lidia Campos; Mirabella, Rossana; de Carvalho-Niebel, Fernanda; Journet, Etienne-Pascal; Ghérardi, Michèle; Huguet, Thierry; Geurts, René; Dénarié, Jean; Rougé, Pierre; Gough, Clare

    2006-09-01

    Rhizobial Nod factors are key symbiotic signals responsible for starting the nodulation process in host legume plants. Of the six Medicago truncatula genes controlling a Nod factor signaling pathway, Nod Factor Perception (NFP) was reported as a candidate Nod factor receptor gene. Here, we provide further evidence for this by showing that NFP is a lysin [corrected] motif (LysM)-receptor-like kinase (RLK). NFP was shown both to be expressed in association with infection thread development and to be involved in the infection process. Consistent with deviations from conserved kinase domain sequences, NFP did not show autophosphorylation activity, suggesting that NFP needs to associate with an active kinase or has unusual functional characteristics different from classical kinases. Identification of nine new M. truncatula LysM-RLK genes revealed a larger family than in the nonlegumes Arabidopsis (Arabidopsis thaliana) or rice (Oryza sativa) of at least 17 members that can be divided into three subfamilies. Three LysM domains could be structurally predicted for all M. truncatula LysM-RLK proteins, whereas one subfamily, which includes NFP, was characterized by deviations from conserved kinase sequences. Most of the newly identified genes were found to be expressed in roots and nodules, suggesting this class of receptors may be more extensively involved in nodulation than was previously known.

  17. Protein kinase A regulation of P2X(4) receptors: requirement for a specific motif in the C-terminus.

    Science.gov (United States)

    Brown, David A; Yule, David I

    2010-02-01

    The P2X purinergic receptor sub-family of ligand-gated ion channels are subject to protein kinase modulation. We have previously demonstrated that P2X(4)R signaling can be positively regulated by increasing intracellular cAMP levels. The molecular mechanism underlying this effect was, however, unknown. The present study initially addressed whether protein kinase A (PKA) activation was required. Subsequently a mutational approach was utilized to determine which region of the receptor was required for this potentiation. In both DT-40 3KO and HEK-293 cells transiently expressing P2X(4)R, forskolin treatment enhanced ATP-mediated signaling. Specific PKA inhibitors prevented the forskolin-induced enhancement of ATP-mediated inward currents in P2X(4)R expressing HEK-293 cells. To define which region of the P2X(4)R was required for the potentiation, mutations were generated in the cytoplasmic C-terminal tail. It was determined that a limited region of the C-terminus, consisting of a non-canonical tyrosine based sorting motif, was required for the effects of PKA. Of note, this region does not harbor any recognizable PKA phosphorylation motifs, and no direct phosphorylation of P2X(4)R was detected, suggesting that PKA phosphorylation of an accessory protein interacts with the endocytosis motif in the C-terminus of the P2X(4)R. In support of this notion, using Total Internal Reflection Fluorescence Microscopy (TIRF)\\ P2X(4)-EGFP was shown to accumulate at/near the plasma membrane following forskolin treatment. In addition, disrupting the endocytosis machinery using a dominant-negative dynamin construct also prevented the PKA-mediated enhancement of ATP-stimulated Ca(2+) signals. Our results are consistent with a novel mechanism of P2XR regulation, whereby PKA activity, without directly phosphorylating P2X(4)R, markedly enhances ATP-stimulated P2X(4)R currents and hence cytosolic Ca(2+) signals. This may occur at least in part, by altering the trafficking of a population of

  18. Interaction of Medicago truncatula Lysin Motif Receptor-Like Kinases, NFP and LYK3, Produced in Nicotiana benthamiana Induces Defence-Like Responses

    NARCIS (Netherlands)

    Pietraszewska-Bogiel, A.; Lefebvre, B.; Koini, A.M.; Klaus-Heisen, D.; Takken, F.L.W.; Geurts, R.; Cullimore, J.V.; Gadella, Th.W.J.

    2013-01-01

    Receptor(-like) kinases with Lysin Motif (LysM) domains in their extracellular region play crucial roles during plant interactions with microorganisms; e.g. Arabidopsis thaliana CERK1 activates innate immunity upon perception of fungal chitin/chitooligosaccharides, whereas Medicago truncatula NFP an

  19. A peptide motif from the second fibronectin module of the neural cell adhesion molecule, NCAM, NLIKQDDGGSPIRHY, is a binding site for the FGF receptor

    DEFF Research Database (Denmark)

    Jacobsen, Jacob Hedemand; Kiselyov, Vladislav; Bock, Elisabeth

    2008-01-01

    The mechanism of fibroblast growth factor receptor (FGFR) activation by the neural cell adhesion molecule (NCAM) is not well understood. A motif in the second NCAM fibronectin type III (FN3) module, termed FGL, has by means of nuclear magnetic resonance (NMR) and surface plasmon resonance (SPR) a...

  20. Predicting Kinase Activity in Angiotensin Receptor Phosphoproteomes Based on Sequence-Motifs and Interactions

    DEFF Research Database (Denmark)

    Bøgebo, Rikke; Horn, Heiko; Olsen, Jesper V;

    2014-01-01

    -arrestin dependent signalling. Two complimentary global phosphoproteomics studies have analyzed the complex signalling induced by the AT1aR. Here we integrate the data sets from these studies and perform a joint analysis using a novel method for prediction of differential kinase activity from phosphoproteomics data......Recent progress in the understanding of seven-transmembrane receptor (7TMR) signalling has promoted the development of a new generation of pathway selective ligands. The angiotensin II type I receptor (AT1aR) is one of the most studied 7TMRs with respect to selective activation of the β...... likely activated kinases. This suggested that AT1aR-dependent signalling activates 48 of the 285 kinases detected in HEK293 cells. Of these, Aurora B, CLK3 and PKG1 have not previously been described in the pathway whereas others, such as PKA, PKB and PKC, are well known. In summary, we have developed...

  1. Anterograde trafficking of G protein-coupled receptors: function of the C-terminal F(X)6LL motif in export from the endoplasmic reticulum.

    Science.gov (United States)

    Duvernay, Matthew T; Dong, Chunmin; Zhang, Xiaoping; Zhou, Fuguo; Nichols, Charles D; Wu, Guangyu

    2009-04-01

    We have reported previously that the F(X)(6)LL motif in the C termini is essential for export of alpha(2B)-adrenergic (alpha(2B)-AR) and angiotensin II type 1 receptors (AT1Rs) from the endoplasmic reticulum (ER). Here, we further demonstrate that mutation of the F(X)(6)LL motif similarly abolished the cell-surface expression of alpha(2B)-AR, AT1R, alpha(1B)-AR, and beta(2)-AR, suggesting that the F(X)(6)LL motif plays a general role in ER export of G protein-coupled receptors (GPCRs). Mutation of Phe to Val, Leu, Trp, and Tyr, and mutation of LL to FF and VV, markedly inhibited alpha(2B)-AR transport, indicating that the F(X)(6)LL function cannot be fully substituted by other hydrophobic residues. The structural analysis revealed that the Phe residue in the F(X)(6)LL motif is buried in the transmembrane domains and possibly interacts with Ile58 in beta(2)-AR and Val42 in alpha(2B)-AR, whereas the LL motif is exposed to the cytosolic space. Indeed, mutation of Ile58 in beta(2)-AR and Val42 in alpha(2B)-AR markedly disrupted cell surface transport of the receptors. It is noteworthy that the Val and Ile residues are highly conserved among the GPCRs carrying the F(X)(6)LL motif. Furthermore, the Phe mutant exhibited a stronger interaction with ER chaperones and was more potently rescued by physical and chemical treatments than the LL mutant. These data suggest that the Phe residue is probably involved in folding of alpha(2B)-AR and beta(2)-AR, possibly through interaction with other hydrophobic residues in neighboring domains. These data also provide the first evidence implying crucial roles of the C termini possibly through modulating multiple events in anterograde trafficking of GPCRs.

  2. Receptor activation and 2 distinct COOH-terminal motifs control G-CSF receptor distribution and internalization kinetics

    NARCIS (Netherlands)

    L.H.J. Aarts (Bart); O. Roovers (Onno); A.C. Ward (Alister); I.P. Touw (Ivo)

    2004-01-01

    textabstractWe have studied the intracellular distribution and internalization kinetics of the granulocyte colony-stimulating factor receptor (G-CSF-R) in living cells using fusion constructs of wild-type or mutant G-CSF-R and enhanced green fluorescent protein (EGFP). Under steady

  3. Downregulation of 5-HT7 Serotonin Receptors by the Atypical Antipsychotics Clozapine and Olanzapine. Role of Motifs in the C-Terminal Domain and Interaction with GASP-1.

    Science.gov (United States)

    Manfra, Ornella; Van Craenenbroeck, Kathleen; Skieterska, Kamila; Frimurer, Thomas; Schwartz, Thue W; Levy, Finn Olav; Andressen, Kjetil Wessel

    2015-07-15

    The human 5-HT7 serotonin receptor, a G-protein-coupled receptor (GPCR), activates adenylyl cyclase constitutively and upon agonist activation. Biased ligands differentially activate 5-HT7 serotonin receptor desensitization, internalization and degradation in addition to G protein activation. We have previously found that the atypical antipsychotics clozapine and olanzapine inhibited G protein activation and, surprisingly, induced both internalization and lysosomal degradation of 5-HT7 receptors. Here, we aimed to determine the mechanism of clozapine- and olanzapine-mediated degradation of 5-HT7 receptors. In the C-terminus of the 5-HT7 receptor, we identified two YXXΦ motifs, LR residues, and a palmitoylated cysteine anchor as potential sites involved in receptor trafficking to lysosomes followed by receptor degradation. Mutating either of these sites inhibited clozapine- and olanzapine-mediated degradation of 5-HT7 receptors and also interfered with G protein activation. In addition, we tested whether receptor degradation was mediated by the GPCR-associated sorting protein-1 (GASP-1). We show that GASP-1 binds the 5-HT7 receptor and regulates the clozapine-mediated degradation. Mutations of the identified motifs and residues, located in or close to Helix-VIII of the 5-HT7 receptor, modified antipsychotic-stimulated binding of proteins (such as GASP-1), possibly by altering the flexibility of Helix-VIII, and also interfered with G protein activation. Taken together, our data demonstrate that binding of clozapine or olanzapine to the 5-HT7 receptor leads to antagonist-mediated lysosomal degradation by exposing key residues in the C-terminal tail that interact with GASP-1.

  4. Corticotropin-Releasing Hormone Receptor Type 1 (CRHR1 Clustering with MAGUKs Is Mediated via Its C-Terminal PDZ Binding Motif.

    Directory of Open Access Journals (Sweden)

    Julia Bender

    Full Text Available The corticotropin-releasing hormone receptor type 1 (CRHR1 plays an important role in orchestrating neuroendocrine, behavioral, and autonomic responses to stress. To identify molecules capable of directly modulating CRHR1 signaling, we performed a yeast-two-hybrid screen using the C-terminal intracellular tail of the receptor as bait. We identified several members of the membrane-associated guanylate kinase (MAGUK family: postsynaptic density protein 95 (PSD95, synapse-associated protein 97 (SAP97, SAP102 and membrane associated guanylate kinase, WW and PDZ domain containing 2 (MAGI2. CRHR1 is co-expressed with the identified MAGUKs and with the additionally investigated PSD93 in neurons of the adult mouse brain and in primary hippocampal neurons, supporting the probability of a physiological interaction in vivo. The C-terminal PDZ (PSD-95, discs large, zona occludens 1 binding motif of CRHR1 is essential for its physical interaction with MAGUKs, as revealed by the CRHR1-STAVA mutant, which harbors a functionally impaired PDZ binding motif. The imitation of a phosphorylation at Thr413 within the PDZ binding motif also disrupted the interaction with MAGUKs. In contrast, distinct PDZ domains within the identified MAGUKs are involved in the interactions. Expression of CRHR1 in primary neurons demonstrated its localization throughout the neuronal plasma membrane, including the excitatory post synapse, where the receptor co-localized with PSD95 and SAP97. The co-expression of CRHR1 and respective interacting MAGUKs in HEK293 cells resulted in a clustered subcellular co-localization which required an intact PDZ binding motif. In conclusion, our study characterized the PDZ binding motif-mediated interaction of CRHR1 with multiple MAGUKs, which directly affects receptor function.

  5. Getting from A to B-exploring the activation motifs of the class B adhesion G protein-coupled receptor subfamily G member 4/GPR112

    DEFF Research Database (Denmark)

    Cornelia Peeters, Miriam; Mos, Iris; Lenselink, Eelke B;

    2016-01-01

    The adhesion G protein-coupled receptors (ADGRs/class B2 G protein-coupled receptors) constitute an ancient family of G protein-coupled receptors that have recently been demonstrated to play important roles in cellular and developmental processes. Here, we describe a first insight...... into the structure-function relationship of ADGRs using the family member ADGR subfamily G member 4 (ADGRG4)/GPR112 as a model receptor. In a bioinformatics approach, we compared conserved, functional elements of the well-characterized class A and class B1 secretin-like G protein-coupled receptors with the ADGRs. We...... identified several potential equivalent motifs and subjected those to mutational analysis. The importance of the mutated residues was evaluated by examining their effect on the high constitutive activity of the N-terminally truncated ADGRG4/GPR112 in a 1-receptor-1-G protein Saccharomyces cerevisiae...

  6. In vivo Regulation of the Allergic Response by the Interleukin 4 Receptor Alpha Chain Immunoreceptor Tyrosine-based Inhibitory Motif

    Science.gov (United States)

    Tachdjian, Raffi; Khatib, Shadi Al; Schwinglshackl, Andreas; Kim, Hong Sook; Chen, Andrew; Blasioli, Julie; Mathias, Clinton; Kim, Hye-Young; Umetsu, Dale T.; Oettgen, Hans C.; Chatila, Talal A.

    2010-01-01

    Background Signaling by IL-4 and IL-13 via the IL-4 receptor alpha chain (IL-4Rα) plays a critical role in the pathology of allergic diseases. The IL-4Rα is endowed with an immunoreceptor tyrosine-based inhibitory motif (ITIM), centered on tyrosine 709 (Y709) in the cytoplasmic domain, that binds a number of regulatory phosphatases. The function of the ITIM in the in vivo regulation of IL-4R signaling remains unknown. Objective To determine the in vivo function of the IL-4Rα ITIM using mice in which the ITIM was inactivated by mutagenesis of the tyrosine Y709 residue into phenylalanine (F709). Methods F709 ITIM mutant mice were derived by knockin mutagenesis. Activation of intracellular signaling cascades by IL-4 and IL-13 was assessed by intracellular staining of phosphorylated signaling intermediates and by gene expression analysis. In vivo responses to allergic sensitization were assessed using models of allergic airway inflammation. Results The F709 mutation increased STAT6 phosphorylation by IL-4 and, disproportionately, by IL-13. This was associated with exaggerated Th2 polarization, enhanced alternative macrophage activation by IL-13, augmented basal and antigen-induced IgE responses and intensified allergen-induced eosinophilic airway inflammation and hyperreactivity. Conclusions These results point to a physiologic negative regulatory role for the Y709 ITIM in signaling via IL-4Rα, especially by IL-13. PMID:20392476

  7. Intracellular localization of the M1 muscarinic acetylcholine receptor through clathrin-dependent constitutive internalization is mediated by a C-terminal tryptophan-based motif.

    Science.gov (United States)

    Uwada, Junsuke; Yoshiki, Hatsumi; Masuoka, Takayoshi; Nishio, Matomo; Muramatsu, Ikunobu

    2014-07-15

    The M1 muscarinic acetylcholine receptor (M1-mAChR, encoded by CHRM1) is a G-protein-coupled membrane receptor that is activated by extracellular cholinergic stimuli. Recent investigations have revealed the intracellular localization of M1-mAChR. In this study, we observed constitutive internalization of M1-mAChR in mouse neuroblastoma N1E-115 cells without agonist stimulation. Constitutive internalization depended on dynamin, clathrin and the adaptor protein-2 (AP-2) complex. A WxxI motif in the M1-mAChR C-terminus is essential for its constitutive internalization, given that replacement of W(442) or I(445) with alanine residues abolished constitutive internalization. This WxxI motif resembles YxxΦ, which is the canonical binding motif for the μ2 subunit of the AP-2 complex. The M1-mAChR C-terminal WxxI motif interacted with AP-2 μ2. W442A and I445A mutants of the M1-mAChR C-terminal sequence lost AP-2-μ2-binding activity, whereas the W442Y mutant bound more effectively than wild type. Consistent with these results, W442A and I445A M1-mAChR mutants selectively localized to the cell surface. By contrast, the W442Y receptor mutant was found only at intracellular sites. Our data indicate that the cellular distribution of M1-mAChR is governed by the C-terminal tryptophan-based motif, which mediates constitutive internalization.

  8. Accessory Interaction Motifs in the Atg19 Cargo Receptor Enable Strong Binding to the Clustered Ubiquitin-related Atg8 Protein.

    Science.gov (United States)

    Abert, Christine; Kontaxis, Georg; Martens, Sascha

    2016-09-02

    Selective autophagy contributes to cellular homeostasis by delivering harmful material into the lysosomal system for degradation via vesicular intermediates referred to as autophagosomes. The cytoplasm-to-vacuole targeting pathway is a variant of selective autophagy in Saccharomyces cerevisiae during which hydrolases such as prApe1 are transported into the vacuole. In general, selectivity is achieved by autophagic cargo receptors that link the cargo to autophagosomal membranes because of their ability to simultaneously interact with the cargo and Atg8 proteins that coat the membrane. The Atg19 receptor contains multiple Atg8 interaction sites in its C terminus in addition to a canonical Atg8-interacting LC3-interacting region (LIR, with LC3 being a homolog of Atg8) motif, but their mode of interaction with Atg8 is unclear. Here we show, using a combination of NMR, microscopy-based interaction assays, and prApe1 processing experiments, that two additional sites interact with Atg8 in a LIR-like and thus mutually exclusive manner. We term these motifs accessory LIR motifs because their affinities are lower than that of the canonical LIR motif. Thus, one Atg19 molecule has the ability to interact with multiple Atg8 proteins simultaneously, resulting in a high-avidity interaction that may confer specific binding to the Atg8-coated autophagosomal membrane on which Atg8 is concentrated.

  9. Site-specific labeling of the type 1 ryanodine receptor using biarsenical fluorophores targeted to engineered tetracysteine motifs.

    Directory of Open Access Journals (Sweden)

    James D Fessenden

    Full Text Available The type 1 ryanodine receptor (RyR1 is an intracellular Ca(2+ release channel that mediates skeletal muscle excitation contraction coupling. While the overall shape of RyR1 has been elucidated using cryo electron microscopic reconstructions, fine structural details remain elusive. To better understand the structure of RyR1, we have previously used a cell-based fluorescence resonance energy transfer (FRET method using a fused green fluorescent protein (GFP donor and a fluorescent acceptor, Cy3NTA that binds specifically to short poly-histidine 'tags' engineered into RyR1. However, the need to permeabilize cells to allow Cy3NTA entry as well as the noncovalent binding of Cy3NTA to the His tag limits future applications of this technique for studying conformational changes of the RyR. To overcome these problems, we used a dodecapeptide sequence containing a tetracysteine (Tc motif to target the biarsenical fluorophores, FlAsH and ReAsH to RyR1. These compounds freely cross intact cell membranes where they then bind covalently to the tetracysteine motif. First, we used this system to conduct FRET measurements in intact cells by fusing a yellow fluorescent protein (YFP FRET donor to the N-terminus of RyR1 and then targeting the FRET acceptor, ReAsH to an adjacent Tc tag. Moderate energy transfer (∼33% was observed whereas ReAsH incubation of a YFPRyR1 fusion protein lacking the Tc tag resulted in no detectable FRET. We also developed a FRET-based system that did not require RyR fluorescent protein fusions by labeling N-terminal Tc-tagged RyR1 with FlAsH, a FRET donor and then targeting the FRET acceptor Cy3NTA to an adjacent decahistidine (His10 tag. A high degree of energy transfer (∼66% indicated proper binding of both compounds to these unique recognition sequences in RyR1. Thus, these two systems should provide unprecedented flexibility in future FRET-based structural determinations of RyR1.

  10. Interaction of Medicago truncatula Lysin Motif Receptor-Like Kinases, NFP and LYK3, Produced in Nicotiana benthamiana Induces Defence-Like Responses

    OpenAIRE

    2013-01-01

    Receptor(-like) kinases with Lysin Motif (LysM) domains in their extracellular region play crucial roles during plant interactions with microorganisms; e.g. Arabidopsis thaliana CERK1 activates innate immunity upon perception of fungal chitin/chitooligosaccharides, whereas Medicago truncatula NFP and LYK3 mediate signalling upon perception of bacterial lipo-chitooligosaccharides, termed Nod factors, during the establishment of mutualism with nitrogen-fixing rhizobia. However, little is still ...

  11. Role of the monocyte chemoattractant protein-1/C-C chemokine receptor 2 signaling pathway in transient receptor potential vanilloid type 1 ablation-induced renal injury in salt-sensitive hypertension.

    Science.gov (United States)

    Wang, Youping; Zhu, Mingjun; Xu, Hui; Cui, Lin; Liu, Weihong; Wang, Xiaoxiao; Shen, Si; Wang, Donna H

    2015-09-01

    Our recent studies indicate that the transient receptor potential vanilloid type 1 (TRPV1) channel may act as a potential regulator of monocyte/macrophage recruitment to reduce renal injury in salt-sensitive hypertension. This study tests the hypothesis that deletion of TRPV1 exaggerates salt-sensitive hypertension-induced renal injury due to enhanced inflammatory responses via monocyte chemoattractant protein-1 (MCP-1)/C-C chemokine receptor 2 (CCR2)-dependent pathways. Wild type (WT) and TRPV1-null mutant (TRPV1(-/-)) mice were subjected to uninephrectomy and deoxycorticosterone acetate (DOCA)-salt treatment for four weeks with or without the selective CCR2 antagonist, RS504393. DOCA-salt treatment increased systolic blood pressure (SBP) to the same degree in both strains, but increased urinary excretion of albumin and 8-isoprostane and decreased creatinine clearance with greater magnitude in TRPV1(-/-) mice compared to WT mice. DOCA-salt treatment also caused renal glomerulosclerosis, tubulointerstitial injury, collagen deposition, monocyte/macrophage infiltration, proinflammatory cytokine and chemokine production, and NF-κB activation in greater degree in TRPV1(-/-) mice compared to WT mice. Blockade of the CCR2 with RS504393 (4 mg/kg/day) had no effect on SBP in DOCA-salt-treated WT or TRPV1(-/-) mice compared to their respective controls. However, treatment with RS504393 ameliorated renal dysfunction and morphological damage, and prevented the increase in monocyte/macrophage infiltration, cytokine/chemokine production, and NF-κB activity in both DOCA-salt hypertensive strains with a greater effect in DOCA-salt-treated TRPV1(-/-) mice compared to DOCA-salt-treated WT mice. No differences in CCR2 protein expression in kidney were found between DOCA-salt-treated WT and TRPV1(-/-) mice with or without RS504393 treatment. Our studies for the first time indicate that deletion of TRPV1 aggravated renal injury in salt-sensitive hypertension via enhancing MCP-1

  12. Hitchcock's Motifs

    NARCIS (Netherlands)

    Walker, Michael

    2005-01-01

    Among the abundant Alfred Hitchcock literature, Hitchcock's Motifs has found a fresh angle. Starting from recurring objects, settings, character-types and events, Michael Walker tracks some forty motifs, themes and clusters across the whole of Hitchcock's oeuvre, including not only all his 52 extant

  13. Peptides from second extracellular loop of C-C chemokine receptor type 5 (CCR5) inhibit diverse strains of HIV-1.

    Science.gov (United States)

    Dogo-Isonagie, Cajetan; Lam, Son; Gustchina, Elena; Acharya, Priyamvada; Yang, Yongping; Shahzad-ul-Hussan, Syed; Clore, G Marius; Kwong, Peter D; Bewley, Carole A

    2012-04-27

    To initiate HIV entry, the HIV envelope protein gp120 must engage its primary receptor CD4 and a coreceptor CCR5 or CXCR4. In the absence of a high resolution structure of a gp120-coreceptor complex, biochemical studies of CCR5 have revealed the importance of its N terminus and second extracellular loop (ECL2) in binding gp120 and mediating viral entry. Using a panel of synthetic CCR5 ECL2-derived peptides, we show that the C-terminal portion of ECL2 (2C, comprising amino acids Cys-178 to Lys-191) inhibit HIV-1 entry of both CCR5- and CXCR4-using isolates at low micromolar concentrations. In functional viral assays, these peptides inhibited HIV-1 entry in a CD4-independent manner. Neutralization assays designed to measure the effects of CCR5 ECL2 peptides when combined with either with the small molecule CD4 mimetic NBD-556, soluble CD4, or the CCR5 N terminus showed additive inhibition for each, indicating that ECL2 binds gp120 at a site distinct from that of N terminus and acts independently of CD4. Using saturation transfer difference NMR, we determined the region of CCR5 ECL2 used for binding gp120, showed that it can bind to gp120 from both R5 and X4 isolates, and demonstrated that the peptide interacts with a CD4-gp120 complex in a similar manner as to gp120 alone. As the CCR5 N terminus-gp120 interactions are dependent on CD4 activation, our data suggest that gp120 has separate binding sites for the CCR5 N terminus and ECL2, the ECL2 binding site is present prior to CD4 engagement, and it is conserved across CCR5- and CXCR4-using strains. These peptides may serve as a starting point for the design of inhibitors with broad spectrum anti-HIV activity.

  14. Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats

    DEFF Research Database (Denmark)

    Dagil, Robert; O'Shea, Charlotte; Nykjær, Anders

    2013-01-01

    megalin and investigated its interaction with gentamicin. Using NMR titration data in HADDOCK, we have generated a three-dimensional model describing the complex between megalin and gentamicin. Gentamicin binds to megalin with low affinity and exploits the common ligand binding motif previously described...

  15. Consensus PP1 binding motifs regulate transcriptional corepression and alternative RNA splicing activities of the steroid receptor coregulators, p54nrb and PSF.

    Science.gov (United States)

    Liu, Liangliang; Xie, Ning; Rennie, Paul; Challis, John R G; Gleave, Martin; Lye, Stephen J; Dong, Xuesen

    2011-07-01

    Originally identified as essential pre-mRNA splicing factors, non-POU-domain-containing, octamer binding protein (p54nrb) and PTB-associated RNA splicing factor (PSF) are also steroid receptor corepressors. The mechanisms by which p54nrb and PSF regulate gene transcription remain unclear. Both p54nrb and PSF contain protein phosphatase 1 (PP1) consensus binding RVxF motifs, suggesting that PP1 may regulate phosphorylation status of p54nrb and PSF and thus their function in gene transcription. In this report, we demonstrated that PP1 forms a protein complex with both p54nrb and PSF. PP1 interacts directly with the RVxF motif only in p54nrb, but not in PSF. Association with PP1 results in dephosphorylation of both p54nrb and PSF in vivo and the loss of their transcriptional corepressor activities. Using the CD44 minigene as a reporter, we showed that PP1 regulates p54nrb and PSF alternative splicing activities that determine exon skipping vs. inclusion in the final mature RNA for translation. In addition, changes in transcriptional corepression and RNA splicing activities of p54nrb and PSF are correlated with alterations in protein interactions of p54nrb and PSF with transcriptional corepressors such as Sin3A and histone deacetylase 1, and RNA splicing factors such as U1A and U2AF. Furthermore, we demonstrated a novel function of the RVxF motif within PSF that enhances its corepression and RNA splicing activities independent of PP1. We conclude that the RVxF motifs play an important role in controlling the multifunctional properties of p54nrb and PSF in the regulation of gene transcription.

  16. ATP regulation of type-1 inositol 1,4,5-trisphosphate receptor activity does not require walker A-type ATP-binding motifs.

    Science.gov (United States)

    Betzenhauser, Matthew J; Wagner, Larry E; Park, Hyung Seo; Yule, David I

    2009-06-12

    ATP is known to increase the activity of the type-1 inositol 1,4,5-trisphosphate receptor (InsP3R1). This effect is attributed to the binding of ATP to glycine rich Walker A-type motifs present in the regulatory domain of the receptor. Only two such motifs are present in neuronal S2+ splice variant of InsP3R1 and are designated the ATPA and ATPB sites. The ATPA site is unique to InsP3R1, and the ATPB site is conserved among all three InsP3R isoforms. Despite the fact that both the ATPA and ATPB sites are known to bind ATP, the relative contribution of these two sites to the enhancing effects of ATP on InsP3R1 function is not known. We report here a mutational analysis of the ATPA and ATPB sites and conclude neither of these sites is required for ATP modulation of InsP3R1. ATP augmented InsP3-induced Ca2+ release from permeabilized cells expressing wild type and ATP-binding site-deficient InsP3R1. Similarly, ATP increased the single channel open probability of the mutated InsP3R1 to the same extent as wild type. ATP likely exerts its effects on InsP3R1 channel function via a novel and as yet unidentified mechanism.

  17. Cutting edge: the nucleotide receptor P2X7 contains multiple protein- and lipid-interaction motifs including a potential binding site for bacterial lipopolysaccharide.

    Science.gov (United States)

    Denlinger, L C; Fisette, P L; Sommer, J A; Watters, J J; Prabhu, U; Dubyak, G R; Proctor, R A; Bertics, P J

    2001-08-15

    The nucleotide receptor P2X7 has been shown to modulate LPS-induced macrophage production of numerous inflammatory mediators. Although the C-terminal portion of P2X7 is thought to be essential for multiple receptor functions, little is known regarding the structural motifs that lie within this region. We show here that the P2X7 C-terminal domain contains several apparent protein-protein and protein-lipid interaction motifs with potential importance to macrophage signaling and LPS action. Surprisingly, P2X7 also contains a conserved LPS-binding domain. In this report, we demonstrate that peptides derived from this P2X7 sequence bind LPS in vitro. Moreover, these peptides neutralize the ability of LPS to activate the extracellular signal-regulated kinases (ERK1, ERK2) and to promote the degradation of the inhibitor of kappaB-alpha isoform (IkappaB-alpha) in RAW 264.7 macrophages. Collectively, these data suggest that the C-terminal domain of P2X7 may directly coordinate several signal transduction events related to macrophage function and LPS action.

  18. Downregulation of 5-HT7 Serotonin Receptors by the Atypical Antipsychotics Clozapine and Olanzapine. Role of Motifs in the C-Terminal Domain and Interaction with GASP-1

    DEFF Research Database (Denmark)

    Manfra, Ornella; Van Craenenbroeck, Kathleen; Skieterska, Kamila;

    2015-01-01

    The human 5-HT7 serotonin receptor, a G-protein-coupled receptor (GPCR), activates adenylyl cyclase constitutively and upon agonist activation. Biased ligands differentially activate 5-HT7 serotonin receptor desensitization, internalization and degradation in addition to G protein activation. We...... have previously found that the atypical antipsychotics clozapine and olanzapine inhibited G protein activation and, surprisingly, induced both internalization and lysosomal degradation of 5-HT7 receptors. Here, we aimed to determine the mechanism of clozapine- and olanzapine-mediated degradation of 5......-HT7 receptors. In the C-terminus of the 5-HT7 receptor, we identified two YXXΦ motifs, LR residues, and a palmitoylated cysteine anchor as potential sites involved in receptor trafficking to lysosomes followed by receptor degradation. Mutating either of these sites inhibited clozapine- and olanzapine...

  19. Positive lymph-node breast cancer patients – activation of NF-κB in tumor-associated leukocytes stimulates cytokine secretion that promotes metastasis via C-C chemokine receptor CCR7.

    Science.gov (United States)

    El-Ghonaimy, Eslam A; El-Shinawi, Mohamed; Ibrahim, Sherif A; El-Ghazaly, Hisham; Abd-El-Tawab, Reda; Nouh, Mohamed A; El-Mamlouk, Tahani; Mohamed, Mona M

    2015-01-01

    Tumor metastasis to lymph nodes is most deadly complication among breast cancer patients. Herein, we investigated the molecular mechanism by which tumor-associated leukocytes (TALs) mediate lymph node metastasis. The density of different leukocyte subtypes infiltrating the tumor microenvironment of negative and positive lymph nodes (nLNs, pLNs) in breast cancer patients was measured using immunohistochemistry. In addition, we isolated TALs from blood drained from the axillary tributaries of nLN and pLN patients during breast surgery. Secretions of TALs were subjected to cytokine profiling using a cytokine antibody array. Our results showed an increase in the number of infiltrated CD45+ cells in the carcinoma tissues of pLN patients with the major proportion being myeloid subsets compared with nLN patients. Furthermore, TALs of pLN patients show a significant fivefold increase in the secretion of interleukin (IL)-1α, interferon-γ, IL-5, IL-3 and tumor necrosis factor-β, and are characterized by enhanced constitutive NF-κB/p65 signaling compared with TALs isolated from nLN patients. Using an invasion assay, cytokines secreted by TALs of pLN patients were shown to augment the invasive phenotype of breast cancer MCF-7 and SKBR3 cells compared with nLN patients. Using flow cytometry, we found that C-C chemokine receptor 7 (CCR7) is significantly overexpressed in breast carcinoma of pLN patients compared with nLNs patients. Intriguingly, CCR7, a mechanistic clue for metastasis, is upregulated in MCF-7 cells upon stimulation with TAL-conditioned media of pLN patients. Our findings show that the molecular cues secreted by TALs alone or in combination with CCR7 may emerge as future therapeutic targets for lymph node metastasis in breast cancer patients.

  20. The Medicago truncatula lysine motif-receptor-like kinase gene family includes NFP and new nodule-expressed genes

    NARCIS (Netherlands)

    Arrighi, J.F.; Barre, A.; Amor, Ben B.; Bersoult, A.; Campos Soriano, L.; Mirabella, R.; Carvalho-Niebel, de F.; Journet, E.P.; Ghérardi, M.; Huguet, T.; Geurts, R.; Dénarié, J.; Rougé, P.; Gough, C.

    2006-01-01

    Rhizobial Nod factors are key symbiotic signals responsible for starting the nodulation process in host legume plants. Of the six Medicago truncatula genes controlling a Nod factor signaling pathway, Nod Factor Perception (NFP) was reported as a candidate Nod factor receptor gene. Here, we provide f

  1. Structure-Based Analysis of Toxoplasma gondii Profilin: A Parasite-Specific Motif Is Required for Recognition by Toll-Like Receptor 11

    Energy Technology Data Exchange (ETDEWEB)

    K Kucera; A Koblansky; L Saunders; K Frederick; E De La Cruz; S Ghosh; Y Modis

    2011-12-31

    Profilins promote actin polymerization by exchanging ADP for ATP on monomeric actin and delivering ATP-actin to growing filament barbed ends. Apicomplexan protozoa such as Toxoplasma gondii invade host cells using an actin-dependent gliding motility. Toll-like receptor (TLR) 11 generates an innate immune response upon sensing T. gondii profilin (TgPRF). The crystal structure of TgPRF reveals a parasite-specific surface motif consisting of an acidic loop, followed by a long {beta}-hairpin. A series of structure-based profilin mutants show that TLR11 recognition of the acidic loop is responsible for most of the interleukin (IL)-12 secretion response to TgPRF in peritoneal macrophages. Deletion of both the acidic loop and the {beta}-hairpin completely abrogates IL-12 secretion. Insertion of the T. gondii acidic loop and {beta}-hairpin into yeast profilin is sufficient to generate TLR11-dependent signaling. Substitution of the acidic loop in TgPRF with the homologous loop from the apicomplexan parasite Cryptosporidium parvum does not affect TLR11-dependent IL-12 secretion, while substitution with the acidic loop from Plasmodium falciparum results in reduced but significant IL-12 secretion. We conclude that the parasite-specific motif in TgPRF is the key molecular pattern recognized by TLR11. Unlike other profilins, TgPRF slows nucleotide exchange on monomeric rabbit actin and binds rabbit actin weakly. The putative TgPRF actin-binding surface includes the {beta}-hairpin and diverges widely from the actin-binding surfaces of vertebrate profilins.

  2. Secretory TAT-peptide-mediated protein transduction of LIF receptor α-chain distal cytoplasmic motifs into human myeloid HL-60 cells

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Q. [Department of Hyperbaric Medicine, No. 401 Hospital of PLA, Qingdao (China); Department of Histology and Embryology, Faculty of Basic Medical Sciences, Second Military Medical University, Shanghai (China); Xiong, J. [Department of Histology and Embryology, Faculty of Basic Medical Sciences, Second Military Medical University, Shanghai (China); Lu, J. [Office of Medical Education, Training Department, Second Military Medical University, Shanghai (China); Xu, S. [Department of Histology and Embryology, Faculty of Basic Medical Sciences, Second Military Medical University, Shanghai (China); Li, Y. [State Food and Drug Administration of China,Huangdao Branch, Qingdao (China); Zhong, X.P.; Gao, G.K. [Department of Hyperbaric Medicine, No. 401 Hospital of PLA, Qingdao (China); Liu, H.Q. [2Department of Histology and Embryology, Faculty of Basic Medical Sciences, Second Military Medical University, Shanghai (China)

    2012-06-22

    The distal cytoplasmic motifs of leukemia inhibitory factor receptor α-chain (LIFRα-CT3) can independently induce intracellular myeloid differentiation in acute myeloid leukemia (AML) cells by gene transfection; however, there are significant limitations in the potential clinical use of these motifs due to liposome-derived genetic modifications. To produce a potentially therapeutic LIFRα-CT3 with cell-permeable activity, we constructed a eukaryotic expression pcDNA3.0-TAT-CT3-cMyc plasmid with a signal peptide (ss) inserted into the N-terminal that codes for an ss-TAT-CT3-cMyc fusion protein. The stable transfection of Chinese hamster ovary (CHO) cells via this vector and subsequent selection by Geneticin resulted in cell lines that express and secrete TAT-CT3-cMyc. The spent medium of pcDNA3.0-TAT-CT3-cMyc-transfected CHO cells could be purified using a cMyc-epitope-tag agarose affinity chromatography column and could be detected via SDS-PAGE, with antibodies against cMyc-tag. The direct administration of TAT-CT3-cMyc to HL-60 cell culture media caused the enrichment of CT3-cMyc in the cytoplasm and nucleus within 30 min and led to a significant reduction of viable cells (P < 0.05) 8 h after exposure. The advantages of using this mammalian expression system include the ease of generating TAT fusion proteins that are adequately transcripted and the potential for a sustained production of such proteins in vitro for future AML therapy.

  3. The Role of Glutamic or Aspartic Acid in Position Four of the Epitope Binding Motif and Thyrotropin Receptor-Extracellular Domain Epitope Selection in Graves' Disease

    Science.gov (United States)

    Inaba, Hidefumi; Martin, William; Ardito, Matt; De Groot, Anne Searls; De Groot, Leslie J.

    2010-01-01

    Context: Development of Graves' disease (GD) is related to HLA-DRB1*0301 (DR3),and more specifically to arginine at position 74 of the DRB1 molecule. The extracellular domain (ECD) of human TSH receptor (hTSH-R) contains the target antigen. Objective and Design: We analyzed the relation between hTSH-R-ECD peptides and DR molecules to determine whether aspartic acid (D) or glutamic acid (E) at position four in the binding motif influenced selection of functional epitopes. Results: Peptide epitopes from TSH-R-ECD with D or E in position four (D/E+) had higher affinity for binding to DR3 than peptides without D/E (D/E−) (IC50 29.3 vs. 61.4, P = 0.0024). HLA-DR7, negatively correlated with GD, and DRB1*0302 (HLA-DR18), not associated with GD, had different profiles of epitope binding. Toxic GD patients who are DR3+ had higher responses to D/E+ peptides than D/E− peptides (stimulation index 1.42 vs. 1.22, P = 0.028). All DR3+ GD patients (toxic + euthyroid) had higher responses, with borderline significance (Sl; 1.32 vs. 1.18, P = 0.051). Splenocytes of DR3 transgenic mice immunized to TSH-R-ECD responded to D/E+ peptides more than D/E− peptides (stimulation index 1.95 vs. 1.69, P = 0.036). Seven of nine hTSH-R-ECD peptide epitopes reported to be reactive with GD patients' peripheral blood mononuclear cells contain binding motifs with D/E at position four. Conclusions: TSH-R-ECD epitopes with D/E in position four of the binding motif bind more strongly to DRB1*0301 than epitopes that are D/E− and are more stimulatory to GD patients' peripheral blood mononuclear cells and to splenocytes from mice immunized to hTSH-R. These epitopes appear important in immunogenicity to TSH-R due to their favored binding to HLA-DR3, thus increasing presentation to T cells. PMID:20392871

  4. Comparative analysis of evolutionarily conserved motifs of epidermal growth factor receptor 2 (HER2) predicts novel potential therapeutic epitopes

    DEFF Research Database (Denmark)

    Deng, Xiaohong; Zheng, Xuxu; Yang, Huanming;

    2014-01-01

    Overexpression of human epidermal growth factor receptor 2 (HER2) is associated with tumor aggressiveness and poor prognosis in breast cancer. With the availability of therapeutic antibodies against HER2, great strides have been made in the clinical management of HER2 overexpressing breast cancer...... for potential therapeutic application. Thus, this novel computational process for predicting or searching for potential epitopes or key target sites may contribute to epitope-based vaccine and function-selected drug design, especially when x-ray crystal structure protein data is not available....

  5. Interaction of Medicago truncatula lysin motif receptor-like kinases, NFP and LYK3, produced in Nicotiana benthamiana induces defence-like responses.

    Directory of Open Access Journals (Sweden)

    Anna Pietraszewska-Bogiel

    Full Text Available Receptor(-like kinases with Lysin Motif (LysM domains in their extracellular region play crucial roles during plant interactions with microorganisms; e.g. Arabidopsis thaliana CERK1 activates innate immunity upon perception of fungal chitin/chitooligosaccharides, whereas Medicago truncatula NFP and LYK3 mediate signalling upon perception of bacterial lipo-chitooligosaccharides, termed Nod factors, during the establishment of mutualism with nitrogen-fixing rhizobia. However, little is still known about the exact activation and signalling mechanisms of MtNFP and MtLYK3. We aimed at investigating putative molecular interactions of MtNFP and MtLYK3 produced in Nicotiana benthamiana. Surprisingly, heterologous co-production of these proteins resulted in an induction of defence-like responses, which included defence-related gene expression, accumulation of phenolic compounds, and cell death. Similar defence-like responses were observed upon production of AtCERK1 in N. benthamiana leaves. Production of either MtNFP or MtLYK3 alone or their co-production with other unrelated receptor(-like kinases did not induce cell death in N. benthamiana, indicating that a functional interaction between these LysM receptor-like kinases is required for triggering this response. Importantly, structure-function studies revealed that the MtNFP intracellular region, specific features of the MtLYK3 intracellular region (including several putative phosphorylation sites, and MtLYK3 and AtCERK1 kinase activity were indispensable for cell death induction, thereby mimicking the structural requirements of nodulation or chitin-induced signalling. The observed similarity of N. benthamiana response to MtNFP and MtLYK3 co-production and AtCERK1 production suggests the existence of parallels between Nod factor-induced and chitin-induced signalling mediated by the respective LysM receptor(-like kinases. Notably, the conserved structural requirements for MtNFP and MtLYK3 biological

  6. Topotecan inhibits cancer cell migration by down-regulation of chemokine CC motif receptor 7 and matrix metalloproteinases

    Institute of Scientific and Technical Information of China (English)

    Sen-sen LIN; Li SUN; Yan-kai ZHANG; Ren-ping ZHAO; Wen-lu LIANG; Sheng-tao YUAN; Lu-yong ZHANG

    2009-01-01

    Aim: The aim of this study was to investigate the effect of topotecan (TPT) on cancer cell migration.Methods: Growth inhibition of TPT was analyzed by MTT assay, and cancer cell migration was measured by transwell double chamber assay. To verify the effect of TPT on the chemokine receptors CXCR4 and CCR7, quantitative PCR, semi-quantitative PCR and Western blot analysis were performed. The secretion of MMP-2 and MMP-9 was detected by enzyme-linked immunosorbent assay (ELISA) and gelatin zymography. To evaluate possible contributions of CCR7 to MMP secretion, the overexpression vectors pcDNA3.1+-CCR7 and CCR7 siRNA were transiently transfected into MDA-MB-435 cells.Results: TPT inhibited cancer cell migration in a dose-dependent manner. Additionally, TPT significantly decreased the expression of CCR7 in both MDA-MB-435 and MDA-MB-231 cells and moderately reduced the expression of CXCR4 in MDA-MB-435 cells. The secretion of MMPs (MMP-2, MMP-9) was also inhibited by TPT. Overexpression of CCR7 increased the secretion of MMP-2/9 and cancer cell migration, whereas knockdown of CCR7 reduced active MMP-2/9 production and migration of MDA-MB-435 cells.Conclusion: TPT inhibited cancer cell migration by down-regulation of CCR7 and MMPs (MMP-2 and MMP-9).

  7. C/C-PAA与C/C-FA弯曲性能对比%Comparison of Flexural Properties Between C/C-PAA and C/C-FA

    Institute of Scientific and Technical Information of China (English)

    张万强; 赵英民; 王涛; 詹万初

    2014-01-01

    通过PIP工艺制备了C/C-PAA、C/C-FA复合材料,对PAA、FA裂解碳的XRD、浸渍效果以及C/C-PAA和C/C-FA的弯曲强度进行了分析.结果表明:PAA裂解碳的炭质量、浸渍效果较好,C/C-PAA弯曲强度比C/C-FA弯曲强度高34.9%,弯曲模量对比不明显.

  8. Structural motifs of importance for the constitutive activity of the orphan 7TM receptor EBI2: analysis of receptor activation in the absence of an agonist

    DEFF Research Database (Denmark)

    Benned-Jensen, Tau; Rosenkilde, Mette M

    2008-01-01

    ), in the conserved CW/FxP motif in TM 6, acted as negative regulators as Ala substitutions at these positions increased the constitutive activity 5.7- and 2.3-fold, respectively, compared with EBI2 wild type (wt). In contrast, ArgII:20 (Arg87) in TM-2 acted as a positive regulator, as substitution to Ala......, but not to Lys, decreased the constitutive activity more than 7-fold compared with wt EBI2. IleIII:03 (Ile106) is located only 4 A from ArgII:20, and a favorable electrostatic interaction with ArgII:20 was created by introduction of Glu in III:03, given that the activity increased to 4.4-fold of that wt EBI2....... It is noteworthy that swapping these charges by introduction of Glu in II:20 and Arg in III:03 resulted in a 2.7-fold increase compared with wt EBI2, thereby rescuing the two signaling-deficient single mutations, which exhibited a 3.8- to 4.5-fold decrease in constitutive activity. The uncovering...

  9. Studies on molecular properties prediction and histamine H3 receptor affinities of novel ligands with uracil-based motifs.

    Science.gov (United States)

    Lipani, Luca; Odadzic, Dalibor; Weizel, Lilia; Schwed, Johannes-Stephan; Sadek, Bassem; Stark, Holger

    2014-10-30

    The histamine H3 receptor (H3R) plays a role in cognitive and memory processes and is involved in different neurological disorders, including Alzheimer's disease, schizophrenia, and narcolepsy. Therefore, several hH3R antagonists/inverse agonists entered clinical phases for a broad spectrum of mainly centrally occurring diseases. However, many other promising candidates failed due to their pharmacokinetic profile, mostly because of their strong lipophilicity accompanied with low solubility. Analysis of previous potential H3R selective antagonists/inverse agonists, e.g. pitolisant, revealed promising results concerning physicochemical properties and drug-likeness. Herein, a series of new hH3R ligands 8-20 consisting of piperidin-1-yl or piperidin-1-yl-propoxyphenyl coupled to different uracil, thymine, and 5,6-dimethyluracil related moieties, were synthesized, evaluated on their binding properties at the hH3R and the estimation of different physicochemical and drug-likeness properties. Due to the coupling to various positions at pyrimidine-2,4-(1H,3H)-dione, affinity at hH3Rs and drug-likeness parameters have been improved. For instance, compound 9 showed in addition to high affinity at the hH3R (pKi (hH3R) = 8.14) clog S, clog P, LE, LipE, and drug-likeness score values of -4.36, 3.47, 0.34, 4.63, and 1.54, respectively. Also, the methyl substituted analog 17 (pKi (hH3R) = 8.15) revealed LE, LipE and drug-likeness score values of -3.29, 2.47, 0.49, 5.52, and 1.76, respectively.

  10. Ruthenium(II)-Catalyzed C-C Arylations and Alkylations: Decarbamoylative C-C Functionalizations.

    Science.gov (United States)

    Moselage, Marc; Li, Jie; Kramm, Frederik; Ackermann, Lutz

    2017-04-05

    Ruthenium(II)biscarboxylate catalysis enabled selective C-C functionalizations by means of decarbamoylative C-C arylations. The versatility of the ruthenium(II) catalysis was reflected by widely applicable C-C arylations and C-C alkylations of aryl amides, as well as acids with modifiable pyrazoles, through facile organometallic C-C activation.

  11. Scanning mutagenesis in a yeast system delineates the role of the NPxxY(x)(5,6)F motif and helix 8 of the adenosine A(2B) receptor in G protein coupling.

    Science.gov (United States)

    Liu, Rongfang; Nahon, Dennis; le Roy, Beau; Lenselink, Eelke B; IJzerman, Adriaan P

    2015-06-15

    The adenosine receptor subfamily includes four subtypes: the A1, A2A, A2B and A3 receptors, which all belong to the superfamily of G protein-coupled receptors (GPCRs). The adenosine A2B receptor is the least investigated of the adenosine receptors, and the molecular mechanisms of its activation have hardly been explored. We used a single-GPCR-one-G protein yeast screening method in combination with mutagenesis studies, molecular modeling and bio-informatics to investigate the importance of the different amino acid residues of the NPxxY(x)6F motif and helix 8 in the human adenosine A2B receptor (hA2BR) activation. A scanning mutagenesis protocol was employed, yielding 11 single mutations and one double mutation of the NPxxY(x)6F motif and 16 single mutations of helix 8. The amino acid residues P287(7.50), Y290(7.53), R293(7.56) and I304(8.57) were found to be essential, since mutation of these amino acid residues to alanine led to a complete loss of function. Western blot analysis showed that mutant receptor R293(7.56)A was not expressed, whereas the other proteins were. Amino acid residues that are also important in receptor activation are: N286(7.49), V289(7.52), Y292(7.55), N294(8.47), F297(8.50), R298(8.51), H302(8.55) and R307(8.60). The mutation Y290(7.53)F lost 50% of efficacy, while F297(8.50)A behaved similar to wild type receptor. The double mutation, Y290(7.53)F/F297(8.50)Y, lost around 70% of efficacy and displayed a lower potency for the reference agonist 5'-(N-ethylcarboxamido)adenosine (NECA). This study provides new insight into the molecular interplay and impact of TM7 and helix 8 for hA2B receptor activation, which may be extrapolated to other adenosine receptors and possibly to other GPCRs.

  12. Analysis of tandem E-box motifs within human Complement receptor 2 (CR2/CD21) promoter reveals cell specific roles for RP58, E2A, USF and localized chromatin accessibility.

    Science.gov (United States)

    Cruickshank, Mark N; Dods, James; Taylor, Rhonda L; Karimi, Mahdad; Fenwick, Emily J; Quail, Elizabeth A; Rea, Alexander J; Holers, V Michael; Abraham, Lawrence J; Ulgiati, Daniela

    2015-07-01

    Complement receptor 2 (CR2/CD21) plays an important role in the generation of normal B cell immune responses. As transcription appears to be the prime mechanism via which surface CR2/CD21 expression is controlled, understanding transcriptional regulation of this gene will have broader implications to B cell biology. Here we report opposing, cell-context specific control of CR2/CD21 promoter activity by tandem E-box elements, spaced 22 bp apart and within 70 bp of the transcription initiation site. We have identified E2A and USF transcription factors as binding to the distal and proximal E-box sites respectively in CR2-positive B-cells, at a site that is hypersensitive to restriction enzyme digestion compared to non-expressing K562 cells. However, additional unidentified proteins have also been found to bind these functionally important elements. By utilizing a proteomics approach we have identified a repressor protein, RP58, binding the distal E-box motif. Co-transfection experiments using RP58 overexpression constructs demonstrated a specific 10-fold repression of CR2/CD21 transcriptional activity mediated through the distal E-box repressor element. Taken together, our results indicate that repression of the CR2/CD21 promoter can occur through one of the E-box motifs via recruitment of RP58 and other factors to bring about a silenced chromatin context within CR2/CD21 non-expressing cells.

  13. Anomalous absorption in c-C_3H and c-C_3D radicals

    Science.gov (United States)

    Chandra, S.; Shinde, S. V.; Kegel, W. H.; Sedlmayr, E.

    Yamamoto et al. (1987) reported the first detection of the c-C_3H radical in TMC-1 through its transition 2_1 2 rightarrow 1_1 1 at 91.5 GHz. The column density of c-C_3H in TMC-1 was estimated to be 6 times 10^12 cm^-2, which is about one order of magnitude lower than that of the c-C_3H_2 which is ubiquitous in galactic objects. Mangum & Wootten (1990) detected c-C_3H through the transition 1_1 0 rightarrow 1_1 1 at 14.8 GHz in 12 additional galactic objects. The most probable production mechanism of both the c-C_3H and c-C_3H_2 in dark clouds is a common dissociation reaction of the C_3H_3^+ ion (Adams & Smith 1987). Although the c-C_3H is 0.8 eV less stable than its isomer l-C_3H, finding of comparable column densities of both the isomers in TMC-1 suggests that the formation rate for both, c-C_3H and l-C_3H, are of about the same order in the cosmic objects. The existence of a metastable isomer under interstellar conditions is a well known phenomenon in astronomy. The aim of this investigation is a quantitative estimate of relative line intensities under NLTE conditions. For wide ranges of physical parameters, where these molecules may be found, we have solved a set of statistical equilibrium equations coupled with the equations of radiative transfer in an on-the-spot approximation. For c-C_3H, we accounted for 51 energy levels connected by 207 radiative transitions and for c-C_3D, we accounted for 51 energy levels connected by 205 radiative transitions. Our results show that the 3_3 1 rightarrow 3_3 0 transition of c-C_3H and c-C_3D may be found in absorption against the cosmic microwave background (CMB). Furthermore, we found population inversion for the 1_1 0 rightarrow 1_1 1 transition. These findings may be useful in identifying these molecules in other cosmic objects, as well as for the determination of physical parameters in these objects.

  14. The Motif Tracking Algorithm

    CERN Document Server

    Wilson, William; Aickelin, Uwe; 10.1007/s11633.008.0032.0

    2010-01-01

    The search for patterns or motifs in data represents a problem area of key interest to finance and economic researchers. In this paper we introduce the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify unknown motifs of a non specified length which repeat within time series data. The power of the algorithm comes from the fact that it uses a small number of parameters with minimal assumptions regarding the data being examined or the underlying motifs. Our interest lies in applying the algorithm to financial time series data to identify unknown patterns that exist. The algorithm is tested using three separate data sets. Particular suitability to financial data is shown by applying it to oil price data. In all cases the algorithm identifies the presence of a motif population in a fast and efficient manner due to the utilisation of an intuitive symbolic representation. The resulting population of motifs is shown to have considerable potential value for other ap...

  15. The Motif Tracking Algorithm

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The search for patterns or motifs in data represents a problem area of key interest to finance and economic researchers. In this paper, we introduce the motif tracking algorithm (MTA), a novel immune inspired (IS) pattern identification tool that is able to identify unknown motifs of a non specified length which repeat within time series data. The power of the algorithm comes from the fact that it uses a small number of parameters with minimal assumptions regarding the data being examined or the underlying motifs. Our interest lies in applying the algorithm to financial time series data to identify unknown patterns that exist. The algorithm is tested using three separate data sets. Particular suitability to financial data is shown by applying it to oil price data. In all cases, the algorithm identifies the presence of a motif population in a fast and efficient manner due to the utilization of an intuitive symbolic representation.The resulting population of motifs is shown to have considerable potential value for other applications such as forecasting and algorithm seeding.

  16. The arginine of the DRY motif in transmembrane segment III functions as a balancing micro-switch in the activation of the β2-adrenergic receptor

    DEFF Research Database (Denmark)

    Hansen, Louise Valentin; Groenen, Marleen; Nygaard, Rie

    2012-01-01

    (s) signaling, arrestin mobilization, and internalization upon alanine substitutions. Conversely, TyrV:24 appears to play a role in stabilizing the active receptor conformation as loss of function of G(s) signaling, arrestin mobilization, and receptor internalization was observed upon alanine substitution...... of TyrV:24. The loss of function of the TyrV:24 mutant could partly be rescued by alanine substitution of either AspIII:25 or GluVI:-06 in the double mutants. Surprisingly, removal of the side chain of the ArgIII:26 micro-switch itself had no effect on G(s) signaling and internalization and only reduced...

  17. Bacteria binding by DMBT1/SAG/gp-340 is confined to the VEVLXXXXW motif in its scavenger receptor cysteine-rich domains

    DEFF Research Database (Denmark)

    Bikker, Floris J; Ligtenberg, Antoon J M; End, Caroline

    2004-01-01

    The scavenger receptor cysteine-rich (SRCR) proteins form an archaic group of metazoan proteins characterized by the presence of SRCR domains. These proteins are classified in group A and B based on the number of conserved cysteine residues in their SRCR domains, i.e. six for group A and eight fo...

  18. A hallmark of immunoreceptor, the tyrosine-based inhibitory motif ITIM, is present in the G protein-coupled receptor OX1R for orexins and drives apoptosis: a novel mechanism.

    Science.gov (United States)

    Voisin, Thierry; El Firar, Aadil; Rouyer-Fessard, Christiane; Gratio, Valérie; Laburthe, Marc

    2008-06-01

    Orexins acting at the G protein-coupled receptor (GPCR) OX1R have recently been shown to promote dramatic apoptosis in cancer cells. We report here that orexin-induced apoptosis is driven by an immunoreceptor tyrosine-based inhibitory motif (ITIM) (IIY(358)NFL) present in the OX1R. This effect is mediated by SHP-2 phosphatase recruitment via a mechanism that requires Gq protein but is independent of phospholipase C activation. This is based on the following observations: 1) mutation of Y(358) into F abolished orexin-induced tyrosine phosphorylation in ITIM, orexin-induced apoptosis, and uncoupled OX1R from Gq protein in transfected Chinese hamster ovary (CHO) cells; 2) orexin-induced apoptosis in CHO cells expressing recombinant OX1R and in colon cancer cells expressing the native receptor was abolished by treatment with the tyrosine phosphatase inhibitor PAO and by transfection with a dominant-negative mutant of SHP-2; 3) orexins were unable to promote apoptosis in fibroblast cells invalidated for the G alpha q subunit and transfected with OX1R cDNA, whereas they promoted apoptosis in cells equipped with G alpha q and OX1R; and 4) the phospholipase C inhibitor U-73122 blocked orexin-stimulated inositol phosphate formation, whereas it had no effect on orexin-induced apoptosis in CHO cells expressing OX1R. These data unravel a novel mechanism, whereby ITIM-expressing GPCRs may trigger apoptosis.

  19. Structural Phase Transformation (F. C. C. - B. C. C.) in F. C. C. Metals and Their Stability on the Path of Transformation

    Science.gov (United States)

    Öztekýn, Yasemin; Çolakoðlu, Kemal

    1997-08-01

    Because of its importance in Solid-State Physics, Metalurgy, Solid Mechanics and geophysics, theoretical strength calculations are performed to locate the stress-free b.c.c phase on three f.c.c metals (Ca, Pb, Ir). Internal energies correspponding to the unstresed b.c.c. and f.c.c. phase, and the required stress and energy changes for f.c.c.-b.c.c. transformation for these crystals are computed. To determine the range of stability (G stability), the Born criterion is used by calculating the values of deformation connecting the stress-free b.c.c. and stress-free f.c.c. phases of Ca, Pb and Ir. The studied crystals are subjected to unconstrained (100) uniaxial tension in all computations, and E.G.E.P. (Extended generalized exponantial potential) model is used to carry out these calculations.

  20. Visibility graph motifs

    CERN Document Server

    Iacovacci, Jacopo

    2015-01-01

    Visibility algorithms transform time series into graphs and encode dynamical information in their topology, paving the way for graph-theoretical time series analysis as well as building a bridge between nonlinear dynamics and network science. In this work we introduce and study the concept of visibility graph motifs, smaller substructures that appear with characteristic frequencies. We develop a theory to compute in an exact way the motif profiles associated to general classes of deterministic and stochastic dynamics. We find that this simple property is indeed a highly informative and computationally efficient feature capable to distinguish among different dynamics and robust against noise contamination. We finally confirm that it can be used in practice to perform unsupervised learning, by extracting motif profiles from experimental heart-rate series and being able, accordingly, to disentangle meditative from other relaxation states. Applications of this general theory include the automatic classification a...

  1. 1-t-motifs

    CERN Document Server

    Taelman, Lenny

    2009-01-01

    We show that the module of rational points on an abelian t-module E is canonically isomorphic with the module Ext^1(M_E, K[t]) of extensions of the trivial t-motif K[t] by the t-motif M_E associated with E. This generalizes prior results of Anderson and Thakur and of Papanikolas and Ramachandran. In case E is uniformizable then we show that this extension module is canonically isomorphic with the corresponding extension module of Pink-Hodge structures. This situation is formally very similar to Deligne's theory of 1-motifs and we have tried to build up the theory in a way that makes this analogy as clear as possible.

  2. Automatic Network Fingerprinting through Single-Node Motifs

    CERN Document Server

    Echtermeyer, Christoph; Rodrigues, Francisco A; Kaiser, Marcus; 10.1371/journal.pone.0015765

    2011-01-01

    Complex networks have been characterised by their specific connectivity patterns (network motifs), but their building blocks can also be identified and described by node-motifs---a combination of local network features. One technique to identify single node-motifs has been presented by Costa et al. (L. D. F. Costa, F. A. Rodrigues, C. C. Hilgetag, and M. Kaiser, Europhys. Lett., 87, 1, 2009). Here, we first suggest improvements to the method including how its parameters can be determined automatically. Such automatic routines make high-throughput studies of many networks feasible. Second, the new routines are validated in different network-series. Third, we provide an example of how the method can be used to analyse network time-series. In conclusion, we provide a robust method for systematically discovering and classifying characteristic nodes of a network. In contrast to classical motif analysis, our approach can identify individual components (here: nodes) that are specific to a network. Such special nodes...

  3. MHC motif viewer

    DEFF Research Database (Denmark)

    Rapin, Nicolas Philippe Jean-Pierre; Hoof, Ilka; Lund, Ole

    2008-01-01

    . Algorithms that predict which peptides MHC molecules bind have recently been developed and cover many different alleles, but the utility of these algorithms is hampered by the lack of tools for browsing and comparing the specificity of these molecules. We have, therefore, developed a web server, MHC motif...... viewer, that allows the display of the likely binding motif for all human class I proteins of the loci HLA A, B, C, and E and for MHC class I molecules from chimpanzee (Pan troglodytes), rhesus monkey (Macaca mulatta), and mouse (Mus musculus). Furthermore, it covers all HLA-DR protein sequences...

  4. The MHC motif viewer

    DEFF Research Database (Denmark)

    Rapin, Nicolas Philippe Jean-Pierre; Hoof, Ilka; Lund, Ole

    2010-01-01

    of peptides, and knowledge of their binding specificities is important for understanding differences in the immune response between individuals. Algorithms predicting which peptides bind a given MHC molecule have recently been developed with high prediction accuracy. The utility of these algorithms...... is hampered by the lack of tools for browsing and comparing specificity of these molecules. We have developed a Web server, MHC Motif Viewer, which allows the display of the binding motif for MHC class I proteins for human, chimpanzee, rhesus monkey, mouse, and swine, as well as HLA-DR protein sequences...

  5. [Personal motif in art].

    Science.gov (United States)

    Gerevich, József

    2015-01-01

    One of the basic questions of the art psychology is whether a personal motif is to be found behind works of art and if so, how openly or indirectly it appears in the work itself. Analysis of examples and documents from the fine arts and literature allow us to conclude that the personal motif that can be identified by the viewer through symbols, at times easily at others with more difficulty, gives an emotional plus to the artistic product. The personal motif may be found in traumatic experiences, in communication to the model or with other emotionally important persons (mourning, disappointment, revenge, hatred, rivalry, revolt etc.), in self-searching, or self-analysis. The emotions are expressed in artistic activity either directly or indirectly. The intention nourished by the artist's identity (Kunstwollen) may stand in the way of spontaneous self-expression, channelling it into hidden paths. Under the influence of certain circumstances, the artist may arouse in the viewer, consciously or unconsciously, an illusionary, misleading image of himself. An examination of the personal motif is one of the important research areas of art therapy.

  6. TNFα modulates Fibroblast Growth Factor Receptor 2 gene expression through the pRB/E2F1 pathway: identification of a non-canonical E2F binding motif.

    Directory of Open Access Journals (Sweden)

    Sirio D'Amici

    Full Text Available Interactions between epithelium and mesenchyme during wound healing are not fully understood, but Fibroblast Growth Factors (FGFs and their receptors FGFRs are recognized as key elements. FGFR2 gene encodes for two splicing transcript variants, FGFR2-IIIb or Keratinocyte Growth Factor Receptor (KGFR and FGFR2-IIIc, which differ for tissue localization and ligand specificity. Proinflammatory cytokines play an essential role in the regulation of epithelial-mesenchymal interactions, and have been indicated to stimulate FGFs production. Here we demonstrated that upregulation of FGFR2 mRNA and protein expression is induced by the proinflammatory cytokines Tumor Necrosis Factor-α, Interleukin-1β and Interleukin 2. Furthermore, we found that TNFα determines FGFR2 transcriptional induction through activation of pRb, mediated by Raf and/or p38 pathways, and subsequent release of the transcription factor E2F1. Experiments based on FGFR2 promoter serial deletions and site-directed mutagenesis allowed us to identify a minimal responsive element that retains the capacity to be activated by E2F1. Computational analysis indicated that this element is a non-canonical E2F responsive motif. Thus far, the molecular mechanisms of FGFR2 upregulation during wound healing or in pathological events are not known. Our data suggest that FGFR2 expression can be modulated by local recruitment of inflammatory cytokines. Furthermore, since alterations in FGFR2 expression have been linked to the pathogenesis of certain human cancers, these findings could also provide elements for diagnosis and potential targets for novel therapeutic approaches.

  7. Thermoelectric properties of porous SiC/C composites

    NARCIS (Netherlands)

    Fujisawa, Masashi; Hata, Toshimitsu; Kitagawa, Hiroyuki; Bronsveld, Paul; Suzuki, Youki; Hasezaki, Kazuhiro; Noda, Yasutoshi; Imamura, Yuji

    2008-01-01

    We developed a porous SiC/C composite by oxidizing a SiC/C composite made from a mixed powder of wood charcoal and SiO2 (32-45 mu m) by pulse current sintering at 1600 and 1800 degrees C under a N-2 atmosphere. The microstructures of the porous SiC/C composites with oxidation and the SiC/C composite

  8. Bioactive motifs of agouti signal protein.

    Science.gov (United States)

    Virador, V M; Santis, C; Furumura, M; Kalbacher, H; Hearing, V J

    2000-08-25

    The switch between the synthesis of eu- and pheomelanins is modulated by the interaction of two paracrine signaling molecules, alpha-melanocyte stimulating hormone (MSH) and agouti signal protein (ASP), which interact with melanocytes via the MSH receptor (MC1R). Comparison of the primary sequence of ASP with the known MSH pharmacophore provides no suggestion about the putative bioactive domain(s) of ASP. To identify such bioactive motif(s), we synthesized 15-mer peptides that spanned the primary sequence of ASP and determined their effects on the melanogenic activities of murine melanocytes. Northern and Western blotting were used, together with chemical analysis of melanins and enzymatic assays, to identify three distinct bioactive regions of ASP that down-regulate eumelanogenesis. The decrease in eumelanin production was mediated by down-regulation of mRNA levels for tyrosinase and other melanogenic enzymes, as occurs in vivo, and these effects were comparable to those elicited by intact recombinant ASP. Shorter peptides in those motifs were synthesized and their effects on melanogenesis were further investigated. The amino acid arginine, which is present in the MSH peptide pharmacophore (HFRW), is also in the most active domain of ASP (KVARP). Our data suggest that lysines and an arginine (in motifs such as KxxxxKxxR or KxxRxxxxK) are important for the bioactivity of ASP. Identification of the specific ASP epitope that interacts with the MC1R has potential pharmacological applications in treating dysfunctions of skin pigmentation.

  9. Silencing of reversion-inducing cysteine-rich protein with Kazal motifs stimulates hyperplastic phenotypes through activation of epidermal growth factor receptor and hypoxia-inducible factor-2α.

    Directory of Open Access Journals (Sweden)

    You Mie Lee

    Full Text Available Reversion-inducing cysteine-rich protein with Kazal motifs (RECK, a tumor suppressor is down-regulated by the oncogenic signals and hypoxia, but the biological function of RECK in early tumorigenic hyperplastic phenotypes is largely unknown. Knockdown of RECK by small interfering RNA (siRECK or hypoxia significantly promoted cell proliferation in various normal epithelial cells. Hypoxia as well as knockdown of RECK by siRNA increased the cell cycle progression, the levels of cyclin D1 and c-Myc, and the phosphorylation of Rb protein (p-pRb, but decreased the expression of p21(cip1, p27(kip1, and p16(ink4A. HIF-2α was upregulated by knockdown of RECK, indicating HIF-2α is a downstream target of RECK. As knockdown of RECK induced the activation of epidermal growth factor receptor (EGFR and treatment of an EGFR kinase inhibitor, gefitinib, suppressed HIF-2α expression induced by the silencing of RECK, we can suggest that the RECK silenicng-EGFR-HIF-2α axis might be a key molecular mechanism to induce hyperplastic phenotype of epithelial cells. It was also found that shRNA of RECK induced larger and more numerous colonies than control cells in an anchorage-independent colony formation assay. Using a xenograft assay, epithelial cells with stably transfected with shRNA of RECK formed a solid mass earlier and larger than those with control cells in nude mice. In conclusion, the suppression of RECK may promote the development of early tumorigenic hyperplastic characteristics in hypoxic stress.

  10. Understanding Rotation about a C=C Double Bond

    Science.gov (United States)

    Barrows, Susan E.; Eberlein, Thomas H.

    2005-09-01

    In this article, twisting about the C=C double bond and the consequential pyramidalization of sp 2 carbon atoms in alkenes were examined in a molecular modeling study using trans -2-butene as a model system. According to our trans -2-butene model and other similar work, most of the strength of a π bond is retained upon twisting, even for remarkably large C C=C C dihedral angles (up to 90°). The phenomenon of sp 2 carbon atom pyramidalization and preservation of π bond strength upon twisting a C=C double bond is well established in the literature, but is rarely discussed in introductory textbooks. This absence is noteworthy because profound manifestations of this effect do occur in compounds that are covered in an introductory organic chemistry curriculum. We present a simple method of introducing the concept of a flexible C=C π bond into beginning organic chemistry courses. We report the energetic demands of partial twisting about the C=C bond in 2-butene as calculated using DFT, LMP2, and MCSCF methods. Finally, using the results of these calculations, we assessed the degree of strain introduced by the twisted nature of the C=C bond in trans cycloalkenes.

  11. High Affinity Heme Binding to a Heme Regulatory Motif on the Nuclear Receptor Rev-erbβ Leads to Its Degradation and Indirectly Regulates Its Interaction with Nuclear Receptor Corepressor.

    Science.gov (United States)

    Carter, Eric L; Gupta, Nirupama; Ragsdale, Stephen W

    2016-01-29

    Rev-erbα and Rev-erbβ are heme-binding nuclear receptors (NR) that repress the transcription of genes involved in regulating metabolism, inflammation, and the circadian clock. Previous gene expression and co-immunoprecipitation studies led to a model in which heme binding to Rev-erbα recruits nuclear receptor corepressor 1 (NCoR1) into an active repressor complex. However, in contradiction, biochemical and crystallographic studies have shown that heme decreases the affinity of the ligand-binding domain of Rev-erb NRs for NCoR1 peptides. One explanation for this discrepancy is that the ligand-binding domain and NCoR1 peptides used for in vitro studies cannot replicate the key features of the full-length proteins used in cellular studies. However, the combined in vitro and cellular results described here demonstrate that heme does not directly promote interactions between full-length Rev-erbβ (FLRev-erbβ) and an NCoR1 construct encompassing all three NR interaction domains. NCoR1 tightly binds both apo- and heme-replete FLRev-erbβ·DNA complexes; furthermore, heme, at high concentrations, destabilizes the FLRev-erbβ·NCoR1 complex. The interaction between FLRev-erbβ and NCoR1 as well as Rev-erbβ repression at the Bmal1 promoter appear to be modulated by another cellular factor(s), at least one of which is related to the ubiquitin-proteasome pathway. Our studies suggest that heme is involved in regulating the degradation of Rev-erbβ in a manner consistent with its role in circadian rhythm maintenance. Finally, the very slow rate constant (10(-6) s(-1)) of heme dissociation from Rev-erbβ rules out a prior proposal that Rev-erbβ acts as an intracellular heme sensor.

  12. Network motifs in music sequences

    CERN Document Server

    Zanette, Damian H

    2010-01-01

    In this note, I summarize ongoing research on motif distribution in networks built up out of symbolic sequences of Western musical origin. Their motif significance profiles exhibit remarkable consistency over different styles and periods, and define a class that cannot be identified with any of the four "superfamilies" to which most real networks seem to belong. Networks from music sequences possess an unusual abundance of bidirectional connections, due to the inherent reversibility of short musical note patterns. This property contributes to motif significance from both local and large-scale features of musical structure.

  13. Dimorphic motifs in D0 and D1+D2 domains of killer cell Ig-like receptor 3DL1 combine to form receptors with high, moderate, and no avidity for the complex of a peptide derived from HIV and HLA-A*2402.

    Science.gov (United States)

    Sharma, Deepti; Bastard, Karine; Guethlein, Lisbeth A; Norman, Paul J; Yawata, Nobuyo; Yawata, Makoto; Pando, Marcelo; Thananchai, Hathairat; Dong, Tao; Rowland-Jones, Sarah; Brodsky, Frances M; Parham, Peter

    2009-10-01

    Comparison of mutant killer cell Ig-like receptor (KIR) 3DL1*015 substituted at natural positions of variation showed that tryptophan/leucine dimorphism at position 283 uniquely changes receptor conformation and can strongly influence binding of the A24nef tetramer. Dimorphic motifs at positions 2, 47, and 54 in D0 and 182 and 283 in D1+D2 distinguish the two 3DL1 lineages, typified by 3DL1*005 and 3DL1*015. The interlineage recombinant, KIR3DL1*001, combines D0 of 3DL1*005 with D1+D2 of 3DL1*015 and binds A24nef more strongly than either parent. In contrast, the reciprocal recombinant with D0 from 3DL1*015 and D1+D2 from 3DL1*005 cannot bind A24nef. Thus, D0 polymorphism directly affects the avidity of the KIR3DL1 ligand binding site. From these observations, multiple sequence alignment, and homology modeling, we constructed structural models for KIR3DL1 and its complex with A24nef. In these models, D0, D1, and D2 come together to form a binding surface for A24nef, which is contacted by all three Ig-like domains. A central pocket binds arginine 83, the only Bw4 motif residue essential for KIR3DL1 interaction, similar to the binding of lysine 80 in HLA-C by KIR2DL1. Central to this interaction is a salt bridge between arginine 83 of Bw4 and glutamate 282 of 3DL1, which juxtaposes the functionally influential dimorphism at position 283. Further 3DL1 mutants were tested and shown to have A24nef-binding properties consistent with the models. A24nef was not bound by KIR3DS1, the activating counterpart of KIR3DL1. Moreover, introducing any one of three residues specific to KIR3DS1, serine 163, arginine 166, or leucine 199, into 3DL1*015, abrogated A24nef binding.

  14. Comparison of insect kinin analogs with cis-peptide bond, type VI-turn motifs identifies optimal stereochemistry for interaction with a recombinant arthropod kinin receptor from the Southern cattle tick, Boophilus microplus

    Science.gov (United States)

    The multifunctional ‘insect kinins’ share the evolutionarily conserved C-terminal pentapeptide motif Phe-X1-X2-Trp-Gly-NH2, where X1 = His, Asn, Ser, or Tyr and X2 = Ser, Pro, or Ala; and are associated with the regulation of diuresis in a variety of species of insects. We previously reported the f...

  15. Donor Killer Immunoglobulin-Like Receptor Profile Bx1 Imparts a Negative Effect and Centromeric B-Specific Gene Motifs Render a Positive Effect on Standard-Risk Acute Myeloid Leukemia/Myelodysplastic Syndrome Patient Survival after Unrelated Donor Hematopoietic Stem Cell Transplantation.

    Science.gov (United States)

    Bao, Xiaojing; Wang, Miao; Zhou, Huifen; Zhang, Huanhuan; Wu, Xiaojin; Yuan, Xiaoni; Li, Yang; Wu, Depei; He, Jun

    2016-02-01

    Donor killer immunoglobulin-like receptor (KIR) group B profiles (Bx) and homozygous of centromeric motif B (Cen-B/B) are the most preferable KIR gene content motifs for hematopoietic stem cell transplantation (HSCT). The risk of transplant from Bx1 donors and the benefit of the presence of Cen-B (regardless of number) were observed for standard-risk acute myeloid leukemia/myelodysplastic syndrome (AML/MDS) patients in this 4-year retrospective study. A total of 210 Chinese patients who underwent unrelated donor HSCT were investigated. Donor KIR profile Bx was associated with significantly improved overall survival (OS; P = .026) and relapse-free survival (RFS; P = .021) and reduced nonrelapse mortality (NRM; P = .017) in AML/MDS patients. A significantly lower survival rate was observed for transplants from Bx1 donors compared with Bx2, Bx3, and Bx4 donors for patients in first complete remission (n = 82; OS: P = .024; RFS: P = .021). Transplant from donors with Cen-B resulted in improved OS (HR = .256; 95% CI, .084 to .774; P = .016) and RFS (HR = .252; 95% CI, .084 to .758; P = .014) in AML/MDS patients at standard risk. However, this particular effect did not increase with a higher number of Cen-B motifs (cB/B versus cA/B; OS: P = .755; RFS: P = .768). No effect was observed on high-risk AML/MDS, acute lymphoblastic leukemia/non-Hodgkin lymphoma, and chronic myelogenous leukemia patients. Avoiding the selection of HSCT donors of KIR profile Bx1 is strongly advisable for standard-risk AML/MDS patients. The presence of the Cen-B motif rather than its number was more important in donor selection for the Chinese population.

  16. Testing of DLR C/C-SiC and C/C for HIFiRE 8 Scramjet Combustor

    Science.gov (United States)

    Glass, David E.; Capriotti, Diego P.; Reimer, Thomas; Kutemeyer, Marius; Smart, Michael K.

    2014-01-01

    Ceramic Matrix Composites (CMCs) have been proposed for use as lightweight hot structures in scramjet combustors. Previous studies have calculated significant weight savings by utilizing CMCs (active and passive) versus actively cooled metallic scramjet structures. Both a carbon/carbon (C/C) and a carbon/carbon-silicon carbide (C/C-SiC) material fabricated by DLR (Stuttgart, Germany) are being considered for use in a passively cooled combustor design for Hypersonic International Flight Research Experimentation (HIFiRE) 8, a joint Australia / Air Force Research Laboratory hypersonic flight program, expected to fly at Mach 7 for approximately 30 sec, at a dynamic pressure of 55 kilopascals. Flat panels of the DLR C/C and C/C-SiC materials were installed downstream of a hydrogen-fueled, dual-mode scramjet combustor and tested for several minutes at conditions simulating flight at Mach 5 and Mach 6. Gaseous hydrogen fuel was used to fuel the scramjet combustor. The test panels were instrumented with embedded Type K and Type S thermocouples. Zirconia felt insulation was used during some of the tests to reduce heat loss from the back surface and thus increase the heated surface temperature of the C/C-SiC panel approximately 177 C (350 F). The final C/C-SiC panel was tested for three cycles totaling over 135 sec at Mach 6 enthalpy. Slightly more erosion was observed on the C/C panel than the C/C-SiC panels, but both material systems demonstrated acceptable recession performance for the HIFiRE 8 flight.

  17. Motif Yggdrasil: sampling sequence motifs from a tree mixture model.

    Science.gov (United States)

    Andersson, Samuel A; Lagergren, Jens

    2007-06-01

    In phylogenetic foot-printing, putative regulatory elements are found in upstream regions of orthologous genes by searching for common motifs. Motifs in different upstream sequences are subject to mutations along the edges of the corresponding phylogenetic tree, consequently taking advantage of the tree in the motif search is an appealing idea. We describe the Motif Yggdrasil sampler; the first Gibbs sampler based on a general tree that uses unaligned sequences. Previous tree-based Gibbs samplers have assumed a star-shaped tree or partially aligned upstream regions. We give a probabilistic model (MY model) describing upstream sequences with regulatory elements and build a Gibbs sampler with respect to this model. The model allows toggling, i.e., the restriction of a position to a subset of nucleotides, but does not require aligned sequences nor edge lengths, which may be difficult to come by. We apply the collapsing technique to eliminate the need to sample nuisance parameters, and give a derivation of the predictive update formula. We show that the MY model improves the modeling of difficult motif instances and that the use of the tree achieves a substantial increase in nucleotide level correlation coefficient both for synthetic data and 37 bacterial lexA genes. We investigate the sensitivity to errors in the tree and show that using random trees MY sampler still has a performance similar to the original version.

  18. Alkali metal mediated C-C bond coupling reaction.

    Science.gov (United States)

    Tachikawa, Hiroto

    2015-02-14

    Metal catalyzed carbon-carbon (C-C) bond formation is one of the important reactions in pharmacy and in organic chemistry. In the present study, the electron and hole capture dynamics of a lithium-benzene sandwich complex, expressed by Li(Bz)2, have been investigated by means of direct ab-initio molecular dynamics method. Following the electron capture of Li(Bz)2, the structure of [Li(Bz)2](-) was drastically changed: Bz-Bz parallel form was rapidly fluctuated as a function of time, and a new C-C single bond was formed in the C1-C1' position of Bz-Bz interaction system. In the hole capture, the intermolecular vibration between Bz-Bz rings was only enhanced. The mechanism of C-C bond formation in the electron capture was discussed on the basis of theoretical results.

  19. Network motifs provide signatures that characterize metabolism†

    OpenAIRE

    Shellman, Erin R.; Burant, Charles F.; Schnell, Santiago

    2013-01-01

    Motifs are repeating patterns that determine the local properties of networks. In this work, we characterized all 3-node motifs using enzyme commission numbers of the International Union of Biochemistry and Molecular Biology to show that motif abundance is related to biochemical function. Further, we present a comparative analysis of motif distributions in the metabolic networks of 21 species across six kingdoms of life. We found the distribution of motif abundances to be similar between spec...

  20. Efficient C/C++ programming smaller, faster, better

    CERN Document Server

    Heller, Steve

    1994-01-01

    Efficient C/C++ Programming describes a practical, real-world approach to efficient C/C++ programming. Topics covered range from how to save storage using a restricted character set and how to speed up access to records by employing hash coding and caching. A selective mailing list system is used to illustrate rapid access to and rearrangement of information selected by criteria specified at runtime.Comprised of eight chapters, this book begins by discussing factors to consider when deciding whether a program needs optimization. In the next chapter, a supermarket price lookup system is used to

  1. One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs.

    Science.gov (United States)

    Lock, Antonia; Forfar, Rachel; Weston, Cathryn; Bowsher, Leo; Upton, Graham J G; Reynolds, Christopher A; Ladds, Graham; Dixon, Ann M

    2014-12-01

    G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in mammals and facilitate a range of physiological responses triggered by a variety of ligands. GPCRs were thought to function as monomers, however it is now accepted that GPCR homo- and hetero-oligomers also exist and influence receptor properties. The Schizosaccharomyces pombe GPCR Mam2 is a pheromone-sensing receptor involved in mating and has previously been shown to form oligomers in vivo. The first transmembrane domain (TMD) of Mam2 contains a small-XXX-small motif, overrepresented in membrane proteins and well-known for promoting helix-helix interactions. An ortholog of Mam2 in Saccharomyces cerevisiae, Ste2, contains an analogous small-XXX-small motif which has been shown to contribute to receptor homo-oligomerization, localization and function. Here we have used experimental and computational techniques to characterize the role of the small-XXX-small motif in function and assembly of Mam2 for the first time. We find that disruption of the motif via mutagenesis leads to reduction of Mam2 TMD1 homo-oligomerization and pheromone-responsive cellular signaling of the full-length protein. It also impairs correct targeting to the plasma membrane. Mutation of the analogous motif in Ste2 yielded similar results, suggesting a conserved mechanism for assembly. Using co-expression of the two fungal receptors in conjunction with computational models, we demonstrate a functional change in G protein specificity and propose that this is brought about through hetero-dimeric interactions of Mam2 with Ste2 via the complementary small-XXX-small motifs. This highlights the potential of these motifs to affect a range of properties that can be investigated in other GPCRs.

  2. Deformation microstructure and orientation of F.C.C. crystals

    DEFF Research Database (Denmark)

    Liu, Q.; Hansen, N.

    1995-01-01

    The effect of crystallographic orientation on the microstructural evolution in f.c.c. metals with medium to high stacking fault energy is analyzed. This analysis is based on a literature review of the behaviour of single crystals and polycrystals supplemented with an experimental study of cold...

  3. Oxidative electrochemical aryl C-C coupling of spiropyrans

    NARCIS (Netherlands)

    Ivashenko, Oleksii; van Herpt, Jochem T.; Rudolf, Petra; Feringa, Ben L.; Browne, Wesley R.

    2013-01-01

    The isolation and definitive assignment of the species formed upon electrochemical oxidation of nitro-spiropyran (SP) is reported. The oxidative aryl C-C coupling at the indoline moiety of the SP radical cation to form covalent dimers of the ring-closed SP form is demonstrated. The coupling is block

  4. Get more control over your C/C++ service

    CERN Document Server

    CERN. Geneva

    2015-01-01

    Are you looking for a way to better diagnose or monitor your C/C++ programs? Find out more about CMX - a neat, lightweight library (<32Kb) which targets this need. It allows to expose information from inside a process through a simple API, enabling pre-failure detection in combination with your favourite monitoring system.

  5. Interstellar detection of c-C3D2

    CERN Document Server

    Spezzano, S; Schilke, P; Caselli, P; Menten, K M; McCarthy, M C; Bizzocchi, L; Trevino-Morales, S P; Aikawa, Y; Schlemmer, S

    2013-01-01

    We report the first interstellar detection of c-C3D2. The doubly deuterated cyclopropenylidene, a carbene, has been detected toward the starless cores TMC- 1C and L1544 using the IRAM 30m telescope. The J(Ka,Kc) = 3(0,3)-2(1,2), 3(1,3)-2(0,2), and 2(2,1)-1(1,0) transitions of this species have been observed at 3 mm in both sources. The expected 1:2 intensity ratio has been found in the 3(0,3)-2(1,2) and 3(1,3)-2(0,2) lines, belonging to the para and ortho species respectively. We also observed lines of the main species, c-C3H2, the singly deuterated c-C3HD, and the species with one 13C off of the principal axis of the molecule, c-H13CC2H. The lines of c-C3D2 have been observed with high signal to noise ratio, better than 7.5 sigma in TMC-1C and 9 sigma in L1544. The abundance of doubly deuterated cyclopropenylidene with respect to the normal species is found to be (0.4 - 0.8)% in TMC-1C and (1.2 - 2.1)% in L1544. The deuteration of this small hydrocarbon ring is analysed with a comprehensive gas-grain model, ...

  6. Reference: TCA1MOTIF [PLACE

    Lifescience Database Archive (English)

    Full Text Available TCA1MOTIF Goldsbrough AP, Albrecht H, Stratford R Salicylic acid-inducible binding ...of a tobacco nuclear protein to a 10 bp sequence which is highly conserved amongst stress-inducible genes. Plant J 3:563-571 (1993) PubMed: 8220463; ...

  7. DIMORPHIC MOTIFS IN D0 AND D1+D2 DOMAINS OF KIR3DL1 COMBINE TO FORM RECEPTORS WITH HIGH, MODERATE AND NO AVIDITY FOR THE COMPLEX OF A PEPTIDE DERIVED FROM HUMAN IMMUNODEFICIENCY VIRUS AND HLA-A*24021

    OpenAIRE

    Sharma, Deepti; Bastard, Karine; Guethlein, Lisbeth A; Norman, Paul J.; Yawata, Nobuyo; Yawata, Makoto; Pando, Marcelo; Thananchai, Hathairat; Dong, Tao; Rowland-Jones, Sarah; Frances M Brodsky; Parham, Peter

    2009-01-01

    Comparison of mutant KIR3DL1*015 substituted at natural positions of variation showed that tryptophan/leucine dimorphism at position 283 uniquely changes receptor conformation and can strongly influence binding of the A24nef tetramer. Dimorphic motifs at positions 2, 47 and 54 in D0 and 182 and 283 in D1+D2 distinguish the two 3DL1 lineages, typified by 3DL1*005 and 3DL1*015. The inter-lineage recombinant, KIR3DL1*001, combines D0 of 3DL1*005 with D1+D2 of 3DL1*015 and binds A24nef more stron...

  8. Dynamic analysis of C/C composite finger seal

    Institute of Scientific and Technical Information of China (English)

    Chen Guoding; Wang Li’na; Yu Qiangpeng; Su Hua

    2014-01-01

    A seal device as an important component of aeroengines has decisive influence on per-formance, reliability, and working life of aeroengines. With the development of aeroengines, demands on the performance characteristics of seal devices are made strictly. Finger seal as a novel kind of sealing device, recently attracts more and more attentions in academic circles and engineer-ing fields at home and abroad. Research on finger seals has been extensively developed, especially on leakage and wear performances under dynamic conditions. However, it is a pity that the work on finger seals has been limited with a single approach that is improving the performance by structural optimization;in addition, the technology of dynamic analysis on finger seals is weak. Aiming at the problems mentioned above, a distributed mass equivalent dynamic model of finger seals considering the coupling effect of overlaid laminates is established in the present paper, the dynamic perfor-mance of 2.5 dimension C/C composite finger seal is analyzed with the model, and then the effects of fiber bundle density and fiber bundle preparation direction on finger seal’s dynamic performance are discussed, as well as compared with those of Co-based alloy finger seal. The current work is about dynamic analysis of finger seals and application of C/C composite in this paper may have much academic significance and many engineering values for improving research level of finger seal dynamics and exploring feasibility of C/C composite being used for finger seals.

  9. [Study on spectral emissivity of C/C composites].

    Science.gov (United States)

    Zhu, Bo; Cao, Wei-Wei; Jing, Min; Dong, Xing-Guang; Wang, Cheng-Guo

    2009-11-01

    Different types of C/C composites were prepared by conventional molding, and the changes in normal spectral emissivity of samples were tested. The testing results show that spectral emissivity of C/C composite reinforced by short cut carbon fibers is generally higher than the sample reinforced by carbon cloth in the entire 2500-13000nm wavelength region. The structure of short cut carbon fibers is relatively loose and the number of material particles is less than other samples in unit volume, which increases the penetration depth of electromagnetic waves. This is the reason for higher normal spectral emissivity and better heat radiation property. Meanwhile, the test results of normal spectral emissivity for fiber perform and C/C composite samples show that the spectral emissivity of resin carbon is better than fiber carbon because of the difference in microstructure for the two kinds of carbon materials. Laser Raman spectroscopy was employed to analyze the microstructures of different carbon materials, and the results show that because sp3 and sp2 hybrid states of carbon atoms in resin carbon produced more vibration modes, the resin carbon also has higher normal spectral emissivity and better characteristics of heat radiation.

  10. Microstructure of C/C Composites with Different Matrix Carbon

    Directory of Open Access Journals (Sweden)

    LIU Hao

    2016-07-01

    Full Text Available The microstructure of carbon/carbon(C/C composites with different matrix carbon was studied by polarized light microscopy (PLM, scanning electron microscopy (SEM, transmission electron microscopy (TEM and XRD techniques respectively. PLM results indicate that the different matrix carbon exhibits different optical reactivity, and the average optical reactivity is gradually enhanced from normal pitch carbon, smooth laminar of pyrocarbon, rough laminar of pyrocarbon to mesophase pitch carbon; SEM results show that the normal pitch carbon is mainly of grapy structure, the pyrocarbon exhibits like-crinkle lamellar structure, while the mesophase pitch carbon exhibits lamellar banded structure with different shapes. Under HRTEM, the lattice fringes of the mesophase pitch carbon are arranged regularly, is a long range ordered crystal structure, and the preferred orientation is high. The degree of the graphite and the interlayer spacing of the material B (mesophase pitch-based C/C composites are better than that of the material D (pyrocarbon-based C/C composites.

  11. Dynamic analysis of C/C composite finger seal

    Directory of Open Access Journals (Sweden)

    Chen Guoding

    2014-06-01

    Full Text Available A seal device as an important component of aeroengines has decisive influence on performance, reliability, and working life of aeroengines. With the development of aeroengines, demands on the performance characteristics of seal devices are made strictly. Finger seal as a novel kind of sealing device, recently attracts more and more attentions in academic circles and engineering fields at home and abroad. Research on finger seals has been extensively developed, especially on leakage and wear performances under dynamic conditions. However, it is a pity that the work on finger seals has been limited with a single approach that is improving the performance by structural optimization; in addition, the technology of dynamic analysis on finger seals is weak. Aiming at the problems mentioned above, a distributed mass equivalent dynamic model of finger seals considering the coupling effect of overlaid laminates is established in the present paper, the dynamic performance of 2.5 dimension C/C composite finger seal is analyzed with the model, and then the effects of fiber bundle density and fiber bundle preparation direction on finger seal’s dynamic performance are discussed, as well as compared with those of Co-based alloy finger seal. The current work is about dynamic analysis of finger seals and application of C/C composite in this paper may have much academic significance and many engineering values for improving research level of finger seal dynamics and exploring feasibility of C/C composite being used for finger seals.

  12. Main: TCA1MOTIF [PLACE

    Lifescience Database Archive (English)

    Full Text Available TCA1MOTIF S000159 17-May-1998 (last modified) kehi TCA-1 (tobacco nuclear protein 1...) binding site; Related to salicylic acid-inducible expression of many genes; Found in barley beta-1,3-gluca...nase and over 30 different plant genes which are known to be induced by one or more forms of stress; A similar sequence (TCA... et al., 1997); SA; salicylic acid; stress; TCA-1; barley (Hordeum vulgare); tobacco (Nicotiana tabacum); TCATCTTCTT ...

  13. Borane-catalyzed cracking of C-C bonds in coal; Boran-katalysierte C-C-Bindungungsspaltung in Steinkohle

    Energy Technology Data Exchange (ETDEWEB)

    Narangerel, J.; Haenel, M.W. [Max-Planck-Institut fuer Kohlenforschung, Muelheim an der Ruhr (Germany)

    1998-09-01

    Coal, especially coking coal, was reacted with hydrogen at comparatively mild reaction conditions (150-280 degrees centigrade, 20 MPa hydrogen pressure) in the presence of catalysts consisting of borange reagents and certain transition metal halides to obtaine more than 80 percent of pyridine-soluble products. The influence of the degree of coalification, catalyst and temperature on the borane-catalyzed hydrogenolysis of C-C bonds in coal was investigated. (orig.) [Deutsch] Steinkohlen, insbesondere im Inkohlungsbereich der Fettkohlen (Kokskohlen), werden in Gegenwart von Katalysatoren aus Boran-Reagentien und bestimmten Uebergangsmetallhalogeniden mit Wasserstoff bei vergleichsweise milden Reaktionsbedingungen (250-280 C, 20 MPa Wasserstoffdruck) in zu ueber 80% pyridinloesliche Produkte umgewandelt. Der Einfluss von Inkohlungsgrad, Katalysator und Temperatur auf die Boran-katalysierte C-C-Bindungshydrogenolyse in Kohle wurde untersucht. (orig.)

  14. Comprehensive discovery of DNA motifs in 349 human cells and tissues reveals new features of motifs.

    Science.gov (United States)

    Zheng, Yiyu; Li, Xiaoman; Hu, Haiyan

    2015-01-01

    Comprehensive motif discovery under experimental conditions is critical for the global understanding of gene regulation. To generate a nearly complete list of human DNA motifs under given conditions, we employed a novel approach to de novo discover significant co-occurring DNA motifs in 349 human DNase I hypersensitive site datasets. We predicted 845 to 1325 motifs in each dataset, for a total of 2684 non-redundant motifs. These 2684 motifs contained 54.02 to 75.95% of the known motifs in seven large collections including TRANSFAC. In each dataset, we also discovered 43 663 to 2 013 288 motif modules, groups of motifs with their binding sites co-occurring in a significant number of short DNA regions. Compared with known interacting transcription factors in eight resources, the predicted motif modules on average included 84.23% of known interacting motifs. We further showed new features of the predicted motifs, such as motifs enriched in proximal regions rarely overlapped with motifs enriched in distal regions, motifs enriched in 5' distal regions were often enriched in 3' distal regions, etc. Finally, we observed that the 2684 predicted motifs classified the cell or tissue types of the datasets with an accuracy of 81.29%. The resources generated in this study are available at http://server.cs.ucf.edu/predrem/.

  15. Noncoding RNA danger motifs bridge innate and adaptive immunity and are potent adjuvants for vaccination

    OpenAIRE

    Wang, Lilin; Smith, Dan; Bot, Simona; Dellamary, Luis; Bloom, Amy; Bot, Adrian

    2002-01-01

    The adaptive immune response is triggered by recognition of T and B cell epitopes and is influenced by “danger” motifs that act via innate immune receptors. This study shows that motifs associated with noncoding RNA are essential features in the immune response reminiscent of viral infection, mediating rapid induction of proinflammatory chemokine expression, recruitment and activation of antigen-presenting cells, modulation of regulatory cytokines, subsequent differentiation of Th1 cells, iso...

  16. seeMotif: exploring and visualizing sequence motifs in 3D structures

    OpenAIRE

    2009-01-01

    Sequence motifs are important in the study of molecular biology. Motif discovery tools efficiently deliver many function related signatures of proteins and largely facilitate sequence annotation. As increasing numbers of motifs are detected experimentally or predicted computationally, characterizing the functional roles of motifs and identifying the potential synergetic relationships between them are important next steps. A good way to investigate novel motifs is to utilize the abundant 3D st...

  17. Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin

    NARCIS (Netherlands)

    Dagil, R.; O'Shea, C.; Nykjaer, A.; Bonvin, A.M.J.J.; Kragelund, B.B.

    2013-01-01

    Gentamicin is an aminoglycoside widely used in treatments of, in particular, enterococcal, mycobacterial, and severe Gram-negative bacterial infections. Large doses of gentamicin cause nephrotoxicity and ototoxicity, entering the cell via the receptor megalin. Until now, no structural information ha

  18. Identification of a novel immunoreceptor tyrosine-based activation motif-containing molecule, STAM2, by mass spectrometry and its involvement in growth factor and cytokine receptor signaling pathways

    DEFF Research Database (Denmark)

    Pandey, A; Fernandez, M M; Steen, H;

    2000-01-01

    In an effort to clone novel tyrosine-phosphorylated substrates of the epidermal growth factor receptor, we have initiated an approach coupling affinity purification using anti-phosphotyrosine antibodies to mass spectrometry-based identification. Here, we report the identification of a signaling m...

  19. The Role of LORELEI in Pollen Tube Reception at the Interface of the Synergid Cell and Pollen Tube Requires the Modified Eight-Cysteine Motif and the Receptor-Like Kinase FERONIA.

    Science.gov (United States)

    Liu, Xunliang; Castro, Claudia; Wang, Yanbing; Noble, Jennifer; Ponvert, Nathaniel; Bundy, Mark; Hoel, Chelsea; Shpak, Elena; Palanivelu, Ravishankar

    2016-05-01

    In angiosperms, pollen tube reception by the female gametophyte is required for sperm release and double fertilization. In Arabidopsis thaliana lorelei (lre) mutants, pollen tube reception fails in most female gametophytes, which thus remain unfertilized. LRE encodes a putative glycosylphosphatidylinositol (GPI)-anchored surface protein with a modified eight-cysteine motif (M8CM). LRE fused to citrine yellow fluorescent protein (LRE-cYFP) remains functional and localizes to the synergid plasma membrane-rich filiform apparatus, the first point of contact between the pollen tube and the female gametophyte. Structure-function analysis using LRE-cYFP showed that the role of LRE in pollen tube reception requires the M8CM, but not the domains required for GPI anchor addition. Consistently, LRE-cYFP-TM, where GPI anchor addition domains were replaced with a single-pass transmembrane domain, fully complemented the pollen tube reception defect in lre-7 female gametophytes. Ectopically expressed and delivered LRE-cYFP from pollen tubes could non-cell-autonomously complement the pollen tube reception defect in lre female gametophytes, only if they expressed FERONIA. Additionally, pollen tube-expressing LRE variants lacking domains critical for GPI anchor addition also rescued lre female gametophyte function. Therefore, LRE and FERONIA jointly function in pollen tube reception at the interface of the synergid cell and pollen tube.

  20. Microglial Immunoreceptor Tyrosine-Based Activation and Inhibition Motif Signaling in Neuroinflammation

    OpenAIRE

    Bettina Linnartz; Yiner Wang; Harald Neumann

    2010-01-01

    Elimination of extracellular aggregates and apoptotic neural membranes without inflammation is crucial for brain tissue homeostasis. In the mammalian central nervous system, essential molecules in this process are the Fc receptors and the DAP12-associated receptors which both trigger the microglial immunoreceptor tyrosine-based activation motif- (ITAM-) Syk-signaling cascade. Microglial triggering receptor expressed on myeloid cells-2 (TREM2), signal regulatory protein- 1, and complement re...

  1. Assembly of PRR-containing receptors on scaffolds: a model for imidazoline I(1)-receptor action.

    Science.gov (United States)

    Musgrave, I F; Dehle, F C; Piletz, J

    2003-12-01

    IRAS, a putative clone of the I(1)-imidazoline receptor, possesses a proline-rich region (PRR) motif, which might interact with SH3 regions on tyrosine kinases, and an integrin-binding motif. Receptors with a PRR motif can generally assemble onto multi-element signaling complexes (eg., the beta(3)-receptor on the EGF receptor) and thereby modulate signal transduction. Integrins serve as scaffolds for multi-element signaling complexes, similar to that assembled with the EGF receptor. It is therefore possible that IRAS signals through a complex with other receptors.

  2. Statistical tests to compare motif count exceptionalities

    Directory of Open Access Journals (Sweden)

    Vandewalle Vincent

    2007-03-01

    Full Text Available Abstract Background Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. Results We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. Conclusion The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use.

  3. rMotifGen: random motif generator for DNA and protein sequences

    Directory of Open Access Journals (Sweden)

    Hardin C Timothy

    2007-08-01

    Full Text Available Abstract Background Detection of short, subtle conserved motif regions within a set of related DNA or amino acid sequences can lead to discoveries about important regulatory domains such as transcription factor and DNA binding sites as well as conserved protein domains. In order to help assess motif detection algorithms on motifs with varying properties and levels of conservation, we have developed a computational tool, rMotifGen, with the sole purpose of generating a number of random DNA or protein sequences containing short sequence motifs. Each motif consensus can be user-defined, randomly generated, or created from a position-specific scoring matrix (PSSM. Insertions and mutations within these motifs are created according to user-defined parameters and substitution matrices. The resulting sequences can be helpful in mutational simulations and in testing the limits of motif detection algorithms. Results Two implementations of rMotifGen have been created, one providing a graphical user interface (GUI for random motif construction, and the other serving as a command line interface. The second implementation has the added advantages of platform independence and being able to be called in a batch mode. rMotifGen was used to construct sample sets of sequences containing DNA motifs and amino acid motifs that were then tested against the Gibbs sampler and MEME packages. Conclusion rMotifGen provides an efficient and convenient method for creating random DNA or amino acid sequences with a variable number of motifs, where the instance of each motif can be incorporated using a position-specific scoring matrix (PSSM or by creating an instance mutated from its corresponding consensus using an evolutionary model based on substitution matrices. rMotifGen is freely available at: http://bioinformatics.louisville.edu/brg/rMotifGen/.

  4. Measurements of $\\psi(3686) \\to K^{-} \\Lambda \\bar{\\Xi}^{+} +c.c.$ and $\\psi(3686) \\to \\gamma K^{-} \\Lambda \\bar{\\Xi}^{+} +c.c$

    CERN Document Server

    Ablikim, M; Ai, X C; Albayrak, O; Albrecht, M; Ambrose, D J; Amoroso, A; An, F F; An, Q; Bai, J Z; Ferroli, R Baldini; Ban, Y; Bennett, D W; Bennett, J V; Bertani, M; Bettoni, D; Bian, J M; Bianchi, F; Boger, E; Bondarenko, O; Boyko, I; Briere, R A; Cai, H; Cai, X; Cakir, O; Calcaterra, A; Cao, G F; Cetin, S A; Chang, J F; Chelkov, G; Chen, G; Chen, H S; Chen, H Y; Chen, J C; Chen, M L; Chen, S J; Chen, X; Chen, X R; Chen, Y B; Cheng, H P; Chu, X K; Cibinetto, G; Cronin-Hennessy, D; Dai, H L; Dai, J P; Dbeyssi, A; Dedovich, D; Deng, Z Y; Denig, A; Denysenko, I; Destefanis, M; DeMori, F; Ding, Y; Dong, C; Dong, J; Dong, L Y; Dong, M Y; Du, S X; Duan, P F; Fan, J Z; Fang, J; Fang, S S; Fang, X; Fang, Y; Fava, L; Feldbauer, F; Felici, G; Feng, C Q; Fioravanti, E; Fritsch, M; Fu, C D; Gao, Q; Gao, X Y; Gao, Y; Gao, Z; Garzia, I; Geng, C; Goetzen, K; Gong, W X; Gradl, W; Greco, M; Gu, M H; Gu, Y T; Guan, Y H; Guo, A Q; Guo, L B; Guo, Y; Guo, Y P; Haddadi, Z; Hafner, A; Han, S; Han, Y L; Hao, X Q; Harris, F A; He, K L; He, Z Y; Held, T; Heng, Y K; Hou, Z L; Hu, C; Hu, H M; Hu, J F; Hu, T; Hu, Y; Huang, G M; Huang, G S; Huang, H P; Huang, J S; Huang, X T; Huang, Y; Hussain, T; Ji, Q; Ji, Q P; Ji, X B; Ji, X L; Jiang, L L; Jiang, L W; Jiang, X S; Jiao, J B; Jiao, Z; Jin, D P; Jin, S; Johansson, T; Julin, A; Kalantar-Nayestanaki, N; Kang, X L; Kang, X S; Kavatsyuk, M; Ke, B C; Kliemt, R; Kloss, B; Kolcu, O B; Kopf, B; Kornicer, M; Kühn, W; Kupsc, A; Lai, W; Lange, J S; Lara, M; Larin, P; Leng, C; Li, C H; Li, Cheng; Li, D M; Li, F; Li, G; Li, H B; Li, J C; Li, Jin; Li, K; Li, Lei; Li, P R; Li, T; Li, W D; Li, W G; Li, X L; Li, X M; Li, X N; Li, X Q; Li, Z B; Liang, H; Liang, Y F; Liang, Y T; Liao, G R; Lin, D X; Liu, B J; Liu, C X; Liu, F H; Liu, Fang; Liu, Feng; Liu, H B; Liu, H H; Liu, H M; Liu, J; Liu, J P; Liu, J Y; Liu, K; Liu, K Y; Liu, L D; Liu, P L; Liu, Q; Liu, S B; Liu, X; Liu, X X; Liu, Y B; Liu, Z A; Liu, Zhiqiang; Liu, Zhiqing; Loehner, H; Lou, X C; Lu, H J; Lu, J G; Lu, R Q; Lu, Y; Lu, Y P; Luo, C L; Luo, M X; Luo, T; Luo, X L; Lv, M; Lyu, X R; Ma, F C; Ma, H L; Ma, L L; Ma, Q M; Ma, S; Ma, T; Ma, X N; Ma, X Y; Maas, F E; Maggiora, M; Malik, Q A; Mao, Y J; Mao, Z P; Marcello, S; Messchendorp, J G; Min, J; Min, T J; Mitchell, R E; Mo, X H; Mo, Y J; Morales, C Morales; Moriya, K; Muchnoi, N Yu; Muramatsu, H; Nefedov, Y; Nerling, F; Nikolaev, I B; Ning, Z; Nisar, S; Niu, S L; Niu, X Y; Olsen, S L; Ouyang, Q; Pacetti, S; Patteri, P; Pelizaeus, M; Peng, H P; Peters, K; Pettersson, J; Ping, J L; Ping, R G; Poling, R; Pu, Y N; Qi, M; Qian, S; Qiao, C F; Qin, L Q; Qin, N; Qin, X S; Qin, Y; Qin, Z H; Qiu, J F; Rashid, K H; Redmer, C F; Ren, H L; Ripka, M; Rong, G; Ruan, X D; Santoro, V; Sarantsev, A; Savrié, M; Schoenning, K; Schumann, S; Shan, W; Shao, M; Shen, C P; Shen, P X; Shen, X Y; Sheng, H Y; Song, W M; Song, X Y; Sosio, S; Spataro, S; Sun, G X; Sun, J F; Sun, S S; Sun, Y J; Sun, Y Z; Sun, Z J; Sun, Z T; Tang, C J; Tang, X; Tapan, I; Thorndike, E H; Tiemens, M; Toth, D; Ullrich, M; Uman, I; Varner, G S; Wang, B; Wang, B L; Wang, D; Wang, D Y; Wang, K; Wang, L L; Wang, L S; Wang, M; Wang, P; Wang, P L; Wang, Q J; Wang, S G; Wang, W; Wang, X F; Wang, Y D; Wang, Y F; Wang, Y Q; Wang, Z; Wang, Z G; Wang, Z H; Wang, Z Y; Weber, T; Wei, D H; Wei, J B; Weidenkaff, P; Wen, S P; Wiedner, U; Wolke, M; Wu, L H; Wu, Z; Xia, L G; Xia, Y; Xiao, D; Xiao, Z J; Xie, Y G; Xiu, Q L; Xu, G F; Xu, L; Xu, Q J; Xu, Q N; Xu, X P; Yan, L; Yan, W B; Yan, W C; Yan, Y H; Yang, H X; Yang, L; Yang, Y; Yang, Y X; Ye, H; Ye, M; Ye, M H; Yin, J H; Yu, B X; Yu, C X; Yu, H W; Yu, J S; Yuan, C Z; Yuan, W L; Yuan, Y; Yuncu, A; Zafar, A A; Zallo, A; Zeng, Y; Zhang, B X; Zhang, B Y; Zhang, C; Zhang, C C; Zhang, D H; Zhang, H H; Zhang, H Y; Zhang, J J; Zhang, J L; Zhang, J Q; Zhang, J W; Zhang, J Y; Zhang, J Z; Zhang, K; Zhang, L; Zhang, S H; Zhang, X Y; Zhang, Y; Zhang, Y H; Zhang, Y T; Zhang, Z H; Zhang, Z P; Zhang, Z Y; Zhao, G; Zhao, J W; Zhao, J Y; Zhao, J Z; Zhao, Lei; Zhao, Ling; Zhao, M G; Zhao, Q; Zhao, Q W; Zhao, S J; Zhao, T C; Zhao, Y B; Zhao, Z G; Zhemchugov, A; Zheng, B; Zheng, J P; Zheng, W J; Zheng, Y H; Zhong, B; Zhou, L; Zhou, Li; Zhou, X; Zhou, X K; Zhou, X R; Zhou, X Y; Zhu, K; Zhu, K J; Zhu, S; Zhu, X L; Zhu, Y C; Zhu, Y S; Zhu, Z A; Zhuang, J; Zotti, L; Zou, B S; Zou, J H

    2015-01-01

    Using a sample of $1.06\\times10^8\\ \\psip$ events produced in $e^+e^-$ collisions at $\\sqrt{s}$ = 3.686 GeV and collected with the BESIII detector at the BEPCII collider, we present studies of the decays $\\klx+c.c.$ and $\\gklx+c.c.$. We observe two hyperons, $\\Xi(1690)^-$ and $\\Xi(1820)^-$, in the $K^-\\Lambda$ invariant mass distribution in the decay $\\klx+c.c.$ with significances of $4.9 \\sigma$ and $6.2 \\sigma$, respectively. The branching fractions of $\\klx+c.c.$, $\\ksx+c.c.$, $\\psip\\to\\gamma \\chi_{cJ}\\to \\gamma K^- \\Lambda \\bar{\\Xi}^+ +c.c.$ $(J=0,\\ 1,\\ 2)$, and $\\psip\\to \\Xi(1690/1820)^{-} \\bar{\\Xi}^++c.c$ with subsequent decay $\\Xi(1690/1820)^-\\to K^-\\Lambda$ are measured for the first time.

  5. Mirrors fabricated with slightly oxidized C/C composites

    Science.gov (United States)

    Wang, Yongjie; Xu, Liang; Ding, Jiaoteng; Xie, Yongjie; Ma, Zhen

    2016-10-01

    Up to now, traditional materials, such as glass, metal and SiC ceramic, gradually begin to be unsatisfied development of the future mirrors. Designable carbon fiber reinforced composites became optimized material for large aperture lightweight mirrors. Carbon/carbon composites exhibit low thermal expansion and no moisture-absorption expansion problem, therefore, they get particular attention in the space reflector field. Ni was always employed as optical layer in the mirror, however, the coating behaved poor bond with substrate and often peeled off during optical processing. In order to solve this problem, slight oxidation was carried on the C/C composites before Ni plated. The Ni coating exhibited stronger coherence and better finish performance. Finally, a 100mm diameter plane mirror was successful fabricated.

  6. Exon silencing by UAGG motifs in response to neuronal excitation.

    Directory of Open Access Journals (Sweden)

    Ping An

    2007-02-01

    Full Text Available Alternative pre-mRNA splicing plays fundamental roles in neurons by generating functional diversity in proteins associated with the communication and connectivity of the synapse. The CI cassette of the NMDA R1 receptor is one of a variety of exons that show an increase in exon skipping in response to cell excitation, but the molecular nature of this splicing responsiveness is not yet understood. Here we investigate the molecular basis for the induced changes in splicing of the CI cassette exon in primary rat cortical cultures in response to KCl-induced depolarization using an expression assay with a tight neuron-specific readout. In this system, exon silencing in response to neuronal excitation was mediated by multiple UAGG-type silencing motifs, and transfer of the motifs to a constitutive exon conferred a similar responsiveness by gain of function. Biochemical analysis of protein binding to UAGG motifs in extracts prepared from treated and mock-treated cortical cultures showed an increase in nuclear hnRNP A1-RNA binding activity in parallel with excitation. Evidence for the role of the NMDA receptor and calcium signaling in the induced splicing response was shown by the use of specific antagonists, as well as cell-permeable inhibitors of signaling pathways. Finally, a wider role for exon-skipping responsiveness is shown to involve additional exons with UAGG-related silencing motifs, and transcripts involved in synaptic functions. These results suggest that, at the post-transcriptional level, excitable exons such as the CI cassette may be involved in strategies by which neurons mount adaptive responses to hyperstimulation.

  7. Investigations on the 4-Quinolone-3-carboxylic Acid Motif. 7. Synthesis and Pharmacological Evaluation of 4-Quinolone-3-carboxamides and 4-Hydroxy-2-quinolone-3-carboxamides as High Affinity Cannabinoid Receptor 2 (CB2R) Ligands with Improved Aqueous Solubility.

    Science.gov (United States)

    Mugnaini, Claudia; Brizzi, Antonella; Ligresti, Alessia; Allarà, Marco; Lamponi, Stefania; Vacondio, Federica; Silva, Claudia; Mor, Marco; Di Marzo, Vincenzo; Corelli, Federico

    2016-02-11

    4-Quinolone-3-carboxamide derivatives have long been recognized as potent and selective cannabinoid type-2 receptor (CB2R) ligands. With the aim to improve their physicochemical properties, basically aqueous solubility, two different approaches were followed, entailing the substitution of the alkyl chain with a basic replacement or scaffold modification to 4-hydroxy-2-quinolone structure. According to the first approach, compound 6d was obtained, showing slightly reduced receptor affinity (K(i) = 60 nM) compared to the lead compound 4 (0.8 nM) but greatly enhanced solubility (400-3400 times depending on the pH of the medium). On the other hand, shifting from 4-quinolone to 4-hydroxy-2-quinolone structure enabled the discovery of a novel class of CB2R ligands, such as 7b and 7c, characterized by K(i) 1300. At pH 7.4, compound 7c resulted by 100-fold more soluble than 4.

  8. MSDmotif: exploring protein sites and motifs

    Directory of Open Access Journals (Sweden)

    Henrick Kim

    2008-07-01

    Full Text Available Abstract Background Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure. Results We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS protocol. An additional entry point facilitates XML requests with XML responses. Conclusion MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.

  9. Assessment of composite motif discovery methods

    Directory of Open Access Journals (Sweden)

    Johansen Jostein

    2008-02-01

    Full Text Available Abstract Background Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have addressed the problem of single motif discovery – discovering binding motifs for individual transcription factors. In higher organisms, however, transcription factors usually act in combination with nearby bound factors to induce specific regulatory behaviours. Hence, recent focus has shifted from single motifs to the discovery of sets of motifs bound by multiple cooperating transcription factors, so called composite motifs or cis-regulatory modules. Given the large number and diversity of methods available, independent assessment of methods becomes important. Although there have been several benchmark studies of single motif discovery, no similar studies have previously been conducted concerning composite motif discovery. Results We have developed a benchmarking framework for composite motif discovery and used it to evaluate the performance of eight published module discovery tools. Benchmark datasets were constructed based on real genomic sequences containing experimentally verified regulatory modules, and the module discovery programs were asked to predict both the locations of these modules and to specify the single motifs involved. To aid the programs in their search, we provided position weight matrices corresponding to the binding motifs of the transcription factors involved. In addition, selections of decoy matrices were mixed with the genuine matrices on one dataset to test the response of programs to varying levels of noise. Conclusion Although some of the methods tested tended to score somewhat better than others overall, there were still large variations between individual datasets and no single method performed consistently better than the rest in all situations. The variation in performance on individual

  10. receptores

    Directory of Open Access Journals (Sweden)

    Salete Regina Daronco Benetti

    2006-01-01

    Full Text Available Se trata de un estudio etnográfico, que tuvo lo objetivo de interpretar el sistema de conocimiento y del significado atribuidos a la sangre referente a la transfusión sanguínea por los donadores y receptores de un banco de sangre. Para la colecta de las informaciones se observaron los participantes y la entrevista etnográfica se realizó el análisis de dominio, taxonómicos y temáticos. Los dominios culturales fueron: la sangre es vida: fuente de vida y alimento valioso; creencias religiosas: fuentes simbólicas de apoyos; donación sanguínea: un gesto colaborador que exige cuidarse, gratifica y trae felicidad; donación sanguínea: fuente simbólica de inseguridad; estar enfermo es una condición para realizar transfusión sanguínea; transfusión sanguínea: esperanza de vida; Creencias populares: transfusión sanguínea como riesgo para la salud; donadores de sangre: personas benditas; donar y recibir sangre: como significado de felicidad. Temática: “líquido precioso que origina, sostiene, modifica la vida, provoca miedo e inseguridad”.

  11. Fitness for synchronization of network motifs

    DEFF Research Database (Denmark)

    Vega, Y.M.; Vázquez-Prada, M.; Pacheco, A.F.

    2004-01-01

    We study the synchronization of Kuramoto's oscillators in small parts of networks known as motifs. We first report on the system dynamics for the case of a scale-free network and show the existence of a non-trivial critical point. We compute the probability that network motifs synchronize, and fi...

  12. Helix-packing motifs in membrane proteins.

    Science.gov (United States)

    Walters, R F S; DeGrado, W F

    2006-09-12

    The fold of a helical membrane protein is largely determined by interactions between membrane-imbedded helices. To elucidate recurring helix-helix interaction motifs, we dissected the crystallographic structures of membrane proteins into a library of interacting helical pairs. The pairs were clustered according to their three-dimensional similarity (rmsd universe of common transmembrane helix-pairing motifs is relatively simple. The largest cluster, which comprises 29% of the library members, consists of an antiparallel motif with left-handed packing angles, and it is frequently stabilized by packing of small side chains occurring every seven residues in the sequence. Right-handed parallel and antiparallel structures show a similar tendency to segregate small residues to the helix-helix interface but spaced at four-residue intervals. Position-specific sequence propensities were derived for the most populated motifs. These structural and sequential motifs should be quite useful for the design and structural prediction of membrane proteins.

  13. C/C++预处理分析与改进%Improvement on C/C++ Preprocessor

    Institute of Scientific and Technical Information of China (English)

    饶伟

    2006-01-01

    通常的C/C++预处理器是一个宏处理器,在编译前自动地把源文件转换为编译器可识别的形式.传统的预处理方法基于文本行替换,没有考虑到具体的上下文环境.这种预处理机制在文件包含、宏作用域、头文件关系上存在着一些缺陷;会影响工程项目代码重用,降低程序的可维护性、可扩展性等.通过从分析c预处理器缺陷出发,并利用FOG[1]及其语言可以得到一种基于元变量和元函数的语法替换机制的解决方案.

  14. Oxidation Behavior of C/C-SiC Gradient Matrix Composites

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Oxidation behavior of C/C-SiC gradient matrix composites and C/C composites were compared in stationary air. The results show that oxidation threshold of C-SiC materials increases with the amount of SiC particles in the codeposition matrix. Oxidation rate of C/C-SiC gradient matrix composites is significantly lower than that of C/C material. The micro-oxidation process was observed by SEM.

  15. A combinatorial code for splicing silencing: UAGG and GGGG motifs.

    Directory of Open Access Journals (Sweden)

    Kyoungha Han

    2005-05-01

    Full Text Available Alternative pre-mRNA splicing is widely used to regulate gene expression by tuning the levels of tissue-specific mRNA isoforms. Few regulatory mechanisms are understood at the level of combinatorial control despite numerous sequences, distinct from splice sites, that have been shown to play roles in splicing enhancement or silencing. Here we use molecular approaches to identify a ternary combination of exonic UAGG and 5'-splice-site-proximal GGGG motifs that functions cooperatively to silence the brain-region-specific CI cassette exon (exon 19 of the glutamate NMDA R1 receptor (GRIN1 transcript. Disruption of three components of the motif pattern converted the CI cassette into a constitutive exon, while predominant skipping was conferred when the same components were introduced, de novo, into a heterologous constitutive exon. Predominant exon silencing was directed by the motif pattern in the presence of six competing exonic splicing enhancers, and this effect was retained after systematically repositioning the two exonic UAGGs within the CI cassette. In this system, hnRNP A1 was shown to mediate silencing while hnRNP H antagonized silencing. Genome-wide computational analysis combined with RT-PCR testing showed that a class of skipped human and mouse exons can be identified by searches that preserve the sequence and spatial configuration of the UAGG and GGGG motifs. This analysis suggests that the multi-component silencing code may play an important role in the tissue-specific regulation of the CI cassette exon, and that it may serve more generally as a molecular language to allow for intricate adjustments and the coordination of splicing patterns from different genes.

  16. Determinación teórica de parámetros estructurales: Estudio de los isómeros [Al,C,C,C] y [Al,C,C,Si

    OpenAIRE

    García Vivas, María Esmeralda

    2015-01-01

    Se ha llevado a cabo un estudio teórico-computacional sobre distintos isómeros [Al,C,C,C] y [Al,C,C,Si]. El estudio se ha realizado dentro del contexto de la Teoría del Funcional de la Densidad (DFT) empleando el funcional B3LYP y la base aug-cc-pVTZ. Para cada uno de los sistemas estudiados hemos caracterizado estructuras lineales (o cuasilineales), cíclicas bien romboidales o de tipo “fan” y estructuras que contienen un anillo de tres miembros. Además se ha llevado a cabo un análisi d...

  17. The Novel Selective Reduction of the C-C Triple Bond

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A novel reduction system is reported here in which the compounds with terminal C-C triple bond and disubstituted C-C triple bond react with NaBH4/Pd(PPh3)4 in a base condition and only terminal C-C triple bond is reduced.

  18. VARUN: discovering extensible motifs under saturation constraints.

    Science.gov (United States)

    Apostolico, Alberto; Comin, Matteo; Parida, Laxmi

    2010-01-01

    The discovery of motifs in biosequences is frequently torn between the rigidity of the model on one hand and the abundance of candidates on the other hand. In particular, motifs that include wild cards or "don't cares" escalate exponentially with their number, and this gets only worse if a don't care is allowed to stretch up to some prescribed maximum length. In this paper, a notion of extensible motif in a sequence is introduced and studied, which tightly combines the structure of the motif pattern, as described by its syntactic specification, with the statistical measure of its occurrence count. It is shown that a combination of appropriate saturation conditions and the monotonicity of probabilistic scores over regions of constant frequency afford us significant parsimony in the generation and testing of candidate overrepresented motifs. A suite of software programs called Varun is described, implementing the discovery of extensible motifs of the type considered. The merits of the method are then documented by results obtained in a variety of experiments primarily targeting protein sequence families. Of equal importance seems the fact that the sets of all surprising motifs returned in each experiment are extracted faster and come in much more manageable sizes than would be obtained in the absence of saturation constraints.

  19. Detecting Motifs in System Call Sequences

    CERN Document Server

    Wilson, William O; Aickelin, Uwe

    2010-01-01

    The search for patterns or motifs in data represents an area of key interest to many researchers. In this paper we present the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify unknown motifs which repeat within time series data. The power of the algorithm is derived from its use of a small number of parameters with minimal assumptions. The algorithm searches from a completely neutral perspective that is independent of the data being analysed, and the underlying motifs. In this paper the motif tracking algorithm is applied to the search for patterns within sequences of low level system calls between the Linux kernel and the operating system's user space. The MTA is able to compress data found in large system call data sets to a limited number of motifs which summarise that data. The motifs provide a resource from which a profile of executed processes can be built. The potential for these profiles and new implications for security research are highlighted. A...

  20. DIMORPHIC MOTIFS IN D0 AND D1+D2 DOMAINS OF KIR3DL1 COMBINE TO FORM RECEPTORS WITH HIGH, MODERATE AND NO AVIDITY FOR THE COMPLEX OF A PEPTIDE DERIVED FROM HUMAN IMMUNODEFICIENCY VIRUS AND HLA-A*24021

    Science.gov (United States)

    Sharma, Deepti; Bastard, Karine; Guethlein, Lisbeth A.; Norman, Paul J.; Yawata, Nobuyo; Yawata, Makoto; Pando, Marcelo; Thananchai, Hathairat; Dong, Tao; Rowland-Jones, Sarah; Brodsky, Frances M.; Parham, Peter

    2010-01-01

    Comparison of mutant KIR3DL1*015 substituted at natural positions of variation showed that tryptophan/leucine dimorphism at position 283 uniquely changes receptor conformation and can strongly influence binding of the A24nef tetramer. Dimorphic motifs at positions 2, 47 and 54 in D0 and 182 and 283 in D1+D2 distinguish the two 3DL1 lineages, typified by 3DL1*005 and 3DL1*015. The inter-lineage recombinant, KIR3DL1*001, combines D0 of 3DL1*005 with D1+D2 of 3DL1*015 and binds A24nef more strongly than either parent. In contrast, the reciprocal recombinant with D0 from 3DL1*015 and D1+D2 from 3DL1*015 cannot bind A24nef. Thus D0 polymorphism directly affects the avidity of the KIR3DL1 ligand-binding site. From these observations, multiple sequence alignment and homology modeling, we constructed structural models for KIR3DL1 and its complex with A24nef. In these models D0, D1 and D2 come together to form a binding surface for A24nef, which is contacted by all three Ig-like domains. A central pocket binds arginine 83, the only Bw4 motif residue essential for KIR3DL1interaction, similarly to the binding of lysine 80 in HLA-C by KIR2DL1. Central to this interaction is a salt bridge between arginine 83 of Bw4 and glutamate 282 of 3DL1, which juxtaposes the functionally influential dimorphism at position 283. Further 3DL1 mutants were tested and shown to have A24nef binding properties consistent with the models. A24nef was not bound by KIR3DS1, the activating counterpart of KIR3DL1. Moreover, introducing any one of three residues specific to KIR3DS1: serine 163, arginine 166 or leucine 199, into 3DL1*015, abrogated A24nef binding. PMID:19752231

  1. Hunting Motifs in Situla Art

    Directory of Open Access Journals (Sweden)

    Andrej Preložnik

    2013-07-01

    Full Text Available Situla art developed as an echo of the toreutic style which had spread from the Near East through the Phoenicians, Greeks and Etruscans as far as the Veneti, Raeti, Histri, and their eastern neighbours in the region of Dolenjska (Lower Carniola. An Early Iron Age phenomenon (c. 600—300 BC, it rep- resents the major and most arresting form of the contemporary visual arts in an area stretching from the foot of the Apennines in the south to the Drava and Sava rivers in the east. Indeed, individual pieces have found their way across the Alpine passes and all the way north to the Danube. In the world and art of the situlae, a prominent role is accorded to ani- mals. They are displayed in numerous representations of human activities on artefacts crafted in the classic situla style – that is, between the late 6th  and early 5th centuries BC – as passive participants (e.g. in pageants or in harness or as an active element of the situla narrative. The most typical example of the latter is the hunting scene. Today we know at least four objects decorat- ed exclusively with hunting themes, and a number of situlae and other larger vessels where hunting scenes are embedded in composite narratives. All this suggests a popularity unparallelled by any other genre. Clearly recognisable are various hunting techniques and weapons, each associated with a particu- lar type of game (Fig. 1. The chase of a stag with javelin, horse and hound is depicted on the long- familiar and repeatedly published fibula of Zagorje (Fig. 2. It displays a hound mauling the stag’s back and a hunter on horseback pursuing a hind, her neck already pierced by the javelin. To judge by the (so far unnoticed shaft end un- der the stag’s muzzle, the hunter would have been brandishing a second jave- lin as well, like the warrior of the Vače fibula or the rider of the Nesactium situla, presumably himself a hunter. Many parallels to his motif are known from Greece, Etruria, and

  2. seeMotif: exploring and visualizing sequence motifs in 3D structures.

    Science.gov (United States)

    Chang, Darby Tien-Hao; Chien, Ting-Ying; Chen, Chien-Yu

    2009-07-01

    Sequence motifs are important in the study of molecular biology. Motif discovery tools efficiently deliver many function related signatures of proteins and largely facilitate sequence annotation. As increasing numbers of motifs are detected experimentally or predicted computationally, characterizing the functional roles of motifs and identifying the potential synergetic relationships between them are important next steps. A good way to investigate novel motifs is to utilize the abundant 3D structures that have also been accumulated at an astounding rate in recent years. This article reports the development of the web service seeMotif, which provides users with an interactive interface for visualizing sequence motifs on protein structures from the Protein Data Bank (PDB). Researchers can quickly see the locations and conformation of multiple motifs among a number of related structures simultaneously. Considering the fact that PDB sequences are usually shorter than those in sequence databases and/or may have missing residues, seeMotif has two complementary approaches for selecting structures and mapping motifs to protein chains in structures. As more and more structures belonging to previously uncharacterized protein families become available, combining sequence and structure information gives good opportunities to facilitate understanding of protein functions in large-scale genome projects. Available at: http://seemotif.csie.ntu.edu.tw,http://seemotif.ee.ncku.edu.tw or http://seemotif.csbb.ntu.edu.tw.

  3. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas.

    Science.gov (United States)

    Petrov, Anton I; Zirbel, Craig L; Leontis, Neocles B

    2013-10-01

    The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson-Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access.

  4. NCBI nr-aa BLAST: CBRC-CFAM-20-0021 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CFAM-20-0021 ref|NP_001001619.1| chemokine (C-C motif) receptor 2 [Sus scrofa]... dbj|BAD08648.1| chemokine (C-C motif) receptor 2 [Sus scrofa] dbj|BAD08655.1| chemokine (C-C motif) receptor 2 [Sus scrofa...] dbj|BAD12134.1| chemokine C-C motif receptor 2 [Sus scrofa] NP_001001619.1 1e-177 82% ...

  5. NCBI nr-aa BLAST: CBRC-CPOR-01-1319 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-CPOR-01-1319 ref|NP_001001619.1| chemokine (C-C motif) receptor 2 [Sus scrofa]... dbj|BAD08648.1| chemokine (C-C motif) receptor 2 [Sus scrofa] dbj|BAD08655.1| chemokine (C-C motif) receptor 2 [Sus scrofa...] dbj|BAD12134.1| chemokine C-C motif receptor 2 [Sus scrofa] NP_001001619.1 1e-154 77% ...

  6. NCBI nr-aa BLAST: CBRC-PVAM-01-1059 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PVAM-01-1059 ref|NP_001001619.1| chemokine (C-C motif) receptor 2 [Sus scrofa]... dbj|BAD08648.1| chemokine (C-C motif) receptor 2 [Sus scrofa] dbj|BAD08655.1| chemokine (C-C motif) receptor 2 [Sus scrofa...] dbj|BAD12134.1| chemokine C-C motif receptor 2 [Sus scrofa] NP_001001619.1 5e-40 69% ...

  7. NCBI nr-aa BLAST: CBRC-EEUR-01-0995 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-EEUR-01-0995 ref|NP_001001619.1| chemokine (C-C motif) receptor 2 [Sus scrofa]... dbj|BAD08648.1| chemokine (C-C motif) receptor 2 [Sus scrofa] dbj|BAD08655.1| chemokine (C-C motif) receptor 2 [Sus scrofa...] dbj|BAD12134.1| chemokine C-C motif receptor 2 [Sus scrofa] NP_001001619.1 3e-96 77% ...

  8. NCBI nr-aa BLAST: CBRC-GACU-05-0028 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-GACU-05-0028 ref|NP_001001619.1| chemokine (C-C motif) receptor 2 [Sus scrofa]... dbj|BAD08648.1| chemokine (C-C motif) receptor 2 [Sus scrofa] dbj|BAD08655.1| chemokine (C-C motif) receptor 2 [Sus scrofa...] dbj|BAD12134.1| chemokine C-C motif receptor 2 [Sus scrofa] NP_001001619.1 2e-11 24% ...

  9. NCBI nr-aa BLAST: CBRC-MMUS-09-0220 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MMUS-09-0220 ref|NP_001001619.1| chemokine (C-C motif) receptor 2 [Sus scrofa]... dbj|BAD08648.1| chemokine (C-C motif) receptor 2 [Sus scrofa] dbj|BAD08655.1| chemokine (C-C motif) receptor 2 [Sus scrofa...] dbj|BAD12134.1| chemokine C-C motif receptor 2 [Sus scrofa] NP_001001619.1 1e-171 77% ...

  10. NCBI nr-aa BLAST: CBRC-DNOV-01-0440 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DNOV-01-0440 ref|NP_001001619.1| chemokine (C-C motif) receptor 2 [Sus scrofa]... dbj|BAD08648.1| chemokine (C-C motif) receptor 2 [Sus scrofa] dbj|BAD08655.1| chemokine (C-C motif) receptor 2 [Sus scrofa...] dbj|BAD12134.1| chemokine C-C motif receptor 2 [Sus scrofa] NP_001001619.1 1e-156 72% ...

  11. NCBI nr-aa BLAST: CBRC-OLAT-24-0006 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-OLAT-24-0006 ref|NP_001001619.1| chemokine (C-C motif) receptor 2 [Sus scrofa]... dbj|BAD08648.1| chemokine (C-C motif) receptor 2 [Sus scrofa] dbj|BAD08655.1| chemokine (C-C motif) receptor 2 [Sus scrofa...] dbj|BAD12134.1| chemokine C-C motif receptor 2 [Sus scrofa] NP_001001619.1 1e-24 25% ...

  12. NCBI nr-aa BLAST: CBRC-PTRO-04-0020 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PTRO-04-0020 ref|NP_001001619.1| chemokine (C-C motif) receptor 2 [Sus scrofa]... dbj|BAD08648.1| chemokine (C-C motif) receptor 2 [Sus scrofa] dbj|BAD08655.1| chemokine (C-C motif) receptor 2 [Sus scrofa...] dbj|BAD12134.1| chemokine C-C motif receptor 2 [Sus scrofa] NP_001001619.1 1e-144 76% ...

  13. NCBI nr-aa BLAST: CBRC-TBEL-01-2403 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TBEL-01-2403 ref|NP_001001619.1| chemokine (C-C motif) receptor 2 [Sus scrofa]... dbj|BAD08648.1| chemokine (C-C motif) receptor 2 [Sus scrofa] dbj|BAD08655.1| chemokine (C-C motif) receptor 2 [Sus scrofa...] dbj|BAD12134.1| chemokine C-C motif receptor 2 [Sus scrofa] NP_001001619.1 1e-158 75% ...

  14. Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions

    Directory of Open Access Journals (Sweden)

    Werner Mark

    2008-08-01

    Full Text Available Abstract Background Variations in the influenza Hemagglutinin protein contributes to antigenic drift resulting in decreased efficiency of seasonal influenza vaccines and escape from host immune response. We performed an in silico study to determine characteristics of novel variable and conserved motifs in the Hemagglutinin protein from previously reported H3N2 strains isolated from Hong Kong from 1968–1999 to predict viral motifs involved in significant biological functions. Results 14 MEME blocks were generated and comparative analysis of the MEME blocks identified blocks 1, 2, 3 and 7 to correlate with several biological functions. Analysis of the different Hemagglutinin sequences elucidated that the single block 7 has the highest frequency of amino acid substitution and the highest number of co-mutating pairs. MEME 2 showed intermediate variability and MEME 1 was the most conserved. Interestingly, MEME blocks 2 and 7 had the highest incidence of potential post-translational modifications sites including phosphorylation sites, ASN glycosylation motifs and N-myristylation sites. Similarly, these 2 blocks overlap with previously identified antigenic sites and receptor binding sites. Conclusion Our study identifies motifs in the Hemagglutinin protein with different amino acid substitution frequencies over a 31 years period, and derives relevant functional characteristics by correlation of these motifs with potential post-translational modifications sites, antigenic and receptor binding sites.

  15. Computational design of model scaffold for anion recognition based on the 'C(α) NN' motif.

    Science.gov (United States)

    Sheet, Tridip; Ghosh, Suvankar; Pal, Debnath; Banerjee, Raja

    2017-01-01

    The 'novel phosphate binding 'C(α) NN' motif', consisting of three consecutive amino acid residues, usually occurs in the protein loop regions preceding a helix. Recent computational and complementary biophysical experiments on a series of chimeric peptides containing the naturally occurring 'C(α) NN' motif at the N-terminus of a designed helix establishes that the motif segment recognizes the anion (sulfate and phosphate ions) through local interaction along with extension of the helical conformation which is thermodynamically favored even in a context-free, nonproteinaceous isolated system. However, the strength of the interaction depends on the amino acid sequence/conformation of the motif. Such a locally-mediated recognition of anions validates its intrinsic affinity towards anions and confirms that the affinity for recognition of anions is embedded within the 'local sequence' of the motif. Based on the knowledge gathered on the sequence/structural aspects of the naturally occurring 'C(α) NN' segment, which provides the guideline for rationally engineering model scaffolds, we have modeled a series of templates and investigated their interactions with anions using computational approach. Two of these designed scaffolds show more efficient anion recognition than those of the naturally occurring 'C(α) NN' motif which have been studied. This may provide an avenue in designing better anion receptors suitable for various biochemical applications.

  16. Creation of Hybrid Nanorods From Sequences of Natural Trimeric Fibrous Proteins Using the Fibritin Trimerization Motif

    Science.gov (United States)

    Papanikolopoulou, Katerina; van Raaij, Mark J.; Mitraki, Anna

    Stable, artificial fibrous proteins that can be functionalized open new avenues in fields such as bionanomaterials design and fiber engineering. An important source of inspiration for the creation of such proteins are natural fibrous proteins such as collagen, elastin, insect silks, and fibers from phages and viruses. The fibrous parts of this last class of proteins usually adopt trimeric, β-stranded structural folds and are appended to globular, receptor-binding domains. It has been recently shown that the globular domains are essential for correct folding and trimerization and can be successfully substituted by a very small (27-amino acid) trimerization motif from phage T4 fibritin. The hybrid proteins are correctly folded nanorods that can withstand extreme conditions. When the fibrous part derives from the adenovirus fiber shaft, different tissue-targeting specificities can be engineered into the hybrid proteins, which therefore can be used as gene therapy vectors. The integration of such stable nanorods in devices is also a big challenge in the field of biomechanical design. The fibritin foldon domain is a versatile trimerization motif and can be combined with a variety of fibrous motifs, such as coiled-coil, collagenous, and triple β-stranded motifs, provided the appropriate linkers are used. The combination of different motifs within the same fibrous molecule to create stable rods with multiple functions can even be envisioned. We provide a comprehensive overview of the experimental procedures used for designing, creating, and characterizing hybrid fibrous nanorods using the fibritin trimerization motif.

  17. Chaotic motifs in gene regulatory networks.

    Science.gov (United States)

    Zhang, Zhaoyang; Ye, Weiming; Qian, Yu; Zheng, Zhigang; Huang, Xuhui; Hu, Gang

    2012-01-01

    Chaos should occur often in gene regulatory networks (GRNs) which have been widely described by nonlinear coupled ordinary differential equations, if their dimensions are no less than 3. It is therefore puzzling that chaos has never been reported in GRNs in nature and is also extremely rare in models of GRNs. On the other hand, the topic of motifs has attracted great attention in studying biological networks, and network motifs are suggested to be elementary building blocks that carry out some key functions in the network. In this paper, chaotic motifs (subnetworks with chaos) in GRNs are systematically investigated. The conclusion is that: (i) chaos can only appear through competitions between different oscillatory modes with rivaling intensities. Conditions required for chaotic GRNs are found to be very strict, which make chaotic GRNs extremely rare. (ii) Chaotic motifs are explored as the simplest few-node structures capable of producing chaos, and serve as the intrinsic source of chaos of random few-node GRNs. Several optimal motifs causing chaos with atypically high probability are figured out. (iii) Moreover, we discovered that a number of special oscillators can never produce chaos. These structures bring some advantages on rhythmic functions and may help us understand the robustness of diverse biological rhythms. (iv) The methods of dominant phase-advanced driving (DPAD) and DPAD time fraction are proposed to quantitatively identify chaotic motifs and to explain the origin of chaotic behaviors in GRNs.

  18. Structure and mechanical characterization of DNA i-motif nanowires by molecular dynamics simulation

    CERN Document Server

    Singh, Raghvendra Pratap; Cleri, Fabrizio

    2013-01-01

    We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully relaxed and equilibrated in water. The unusual stacked C*C+ stacked structure, formed by four ssDNA strands arranged in an intercalated tetramer, is here fully characterized both statically and dynamically. By applying stretching, compression and bending deformation with the steered molecular dynamics and umbrella sampling methods, we extract the apparent Young's and bending moduli of the nanowire, as wel as estimates for the tensile strength and persistence length. According to our results, the i-motif nanowire shares similarities with structural proteins, as far as its tensile stiffness, but is closer to nucleic acids and flexible proteins, as far as its bending rigidity is concerned. Furthermore, thanks to its very thin cross section, the apparent tensile toughness is close to...

  19. WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches.

    Science.gov (United States)

    Romer, Katherine A; Kayombya, Guy-Richard; Fraenkel, Ernest

    2007-07-01

    WebMOTIFS provides a web interface that facilitates the discovery and analysis of DNA-sequence motifs. Several studies have shown that the accuracy of motif discovery can be significantly improved by using multiple de novo motif discovery programs and using randomized control calculations to identify the most significant motifs or by using Bayesian approaches. WebMOTIFS makes it easy to apply these strategies. Using a single submission form, users can run several motif discovery programs and score, cluster and visualize the results. In addition, the Bayesian motif discovery program THEME can be used to determine the class of transcription factors that is most likely to regulate a set of sequences. Input can be provided as a list of gene or probe identifiers. Used with the default settings, WebMOTIFS accurately identifies biologically relevant motifs from diverse data in several species. WebMOTIFS is freely available at http://fraenkel.mit.edu/webmotifs.

  20. Structural motifs are closed into cycles in proteins.

    Science.gov (United States)

    Efimov, Alexander V

    2010-08-27

    Beta-hairpins, triple-strand beta-sheets and betaalphabeta-units represent simple structural motifs closed into cycles by systems of hydrogen bonds. Secondary closing of these simple motifs into large cycles by means of different superhelices, split beta-hairpins or SS-bridges results in the formation of more complex structural motifs having unique overall folds and unique handedness such as abcd-units, phi-motifs, five- and seven-segment alpha/beta-motifs. Apparently, the complex structural motifs are more cooperative and stable and this may be one of the main reasons of high frequencies of occurrence of the motifs in proteins.

  1. Functional characterization of variations on regulatory motifs.

    Directory of Open Access Journals (Sweden)

    Michal Lapidot

    2008-03-01

    Full Text Available Transcription factors (TFs regulate gene expression through specific interactions with short promoter elements. The same regulatory protein may recognize a variety of related sequences. Moreover, once they are detected it is hard to predict whether highly similar sequence motifs will be recognized by the same TF and regulate similar gene expression patterns, or serve as binding sites for distinct regulatory factors. We developed computational measures to assess the functional implications of variations on regulatory motifs and to compare the functions of related sites. We have developed computational means for estimating the functional outcome of substituting a single position within a binding site and applied them to a collection of putative regulatory motifs. We predict the effects of nucleotide variations within motifs on gene expression patterns. In cases where such predictions could be compared to suitable published experimental evidence, we found very good agreement. We further accumulated statistics from multiple substitutions across various binding sites in an attempt to deduce general properties that characterize nucleotide substitutions that are more likely to alter expression. We found that substitutions involving Adenine are more likely to retain the expression pattern and that substitutions involving Guanine are more likely to alter expression compared to the rest of the substitutions. Our results should facilitate the prediction of the expression outcomes of binding site variations. One typical important implication is expected to be the ability to predict the phenotypic effect of variation in regulatory motifs in promoters.

  2. Sublinear Time Motif Discovery from Multiple Sequences

    Directory of Open Access Journals (Sweden)

    Yunhui Fu

    2013-10-01

    Full Text Available In this paper, a natural probabilistic model for motif discovery has been used to experimentally test the quality of motif discovery programs. In this model, there are k background sequences, and each character in a background sequence is a random character from an alphabet, Σ. A motif G = g1g2 ... gm is a string of m characters. In each background sequence is implanted a probabilistically-generated approximate copy of G. For a probabilistically-generated approximate copy b1b2 ... bm of G, every character, bi, is probabilistically generated, such that the probability for bi ≠ gi is at most α. We develop two new randomized algorithms and one new deterministic algorithm. They make advancements in the following aspects: (1 The algorithms are much faster than those before. Our algorithms can even run in sublinear time. (2 They can handle any motif pattern. (3 The restriction for the alphabet size is a lower bound of four. This gives them potential applications in practical problems, since gene sequences have an alphabet size of four. (4 All algorithms have rigorous proofs about their performances. The methods developed in this paper have been used in the software implementation. We observed some encouraging results that show improved performance for motif detection compared with other software.

  3. Variants of C-C motif chemokine 22 (CCL22 are associated with susceptibility to atopic dermatitis: case-control studies.

    Directory of Open Access Journals (Sweden)

    Tomomitsu Hirota

    Full Text Available Atopic dermatitis (AD is a common inflammatory skin disease caused by multiple genetic and environmental factors. AD is characterized by the local infiltration of T helper type 2 (Th2 cells. Recent clinical studies have shown important roles of the Th2 chemokines, CCL22 and CCL17 in the pathogenesis of AD. To investigate whether polymorphisms of the CCL22 gene affect the susceptibility to AD, we conducted association studies and functional studies of the related variants. We first resequenced the CCL22 gene and found a total of 39 SNPs. We selected seven tag SNPs in the CCL22 gene, and conducted association studies using two independent Japanese populations (1(st population, 916 cases and 1,032 controls; 2(nd population 1,034 cases and 1,004 controls. After the association results were combined by inverse variance method, we observed a significant association at rs4359426 (meta-analysis, combined P = 9.6×10⁻⁶; OR, 0.74; 95% CI, 0.65-0.85. Functional analysis revealed that the risk allele of rs4359426 contributed to higher expression levels of CCL22 mRNA. We further examined the allelic differences in the binding of nuclear proteins by electrophoretic mobility shift assay. The signal intensity of the DNA-protein complex derived from the G allele of rs223821, which was in absolute LD with rs4359426, was higher than that from the A allele. Although further functional analyses are needed, it is likely that related variants play a role in susceptibility to AD in a gain-of-function manner. Our findings provide a new insight into the etiology and pathogenesis of AD.

  4. Variants of C-C motif chemokine 22 (CCL22) are associated with susceptibility to atopic dermatitis: case-control studies.

    Science.gov (United States)

    Hirota, Tomomitsu; Saeki, Hidehisa; Tomita, Kaori; Tanaka, Shota; Ebe, Kouji; Sakashita, Masafumi; Yamada, Takechiyo; Fujieda, Shigeharu; Miyatake, Akihiko; Doi, Satoru; Enomoto, Tadao; Hizawa, Nobuyuki; Sakamoto, Tohru; Masuko, Hironori; Sasaki, Takashi; Ebihara, Tamotsu; Amagai, Masayuki; Esaki, Hitokazu; Takeuchi, Satoshi; Furue, Masutaka; Noguchi, Emiko; Kamatani, Naoyuki; Nakamura, Yusuke; Kubo, Michiaki; Tamari, Mayumi

    2011-01-01

    Atopic dermatitis (AD) is a common inflammatory skin disease caused by multiple genetic and environmental factors. AD is characterized by the local infiltration of T helper type 2 (Th2) cells. Recent clinical studies have shown important roles of the Th2 chemokines, CCL22 and CCL17 in the pathogenesis of AD. To investigate whether polymorphisms of the CCL22 gene affect the susceptibility to AD, we conducted association studies and functional studies of the related variants. We first resequenced the CCL22 gene and found a total of 39 SNPs. We selected seven tag SNPs in the CCL22 gene, and conducted association studies using two independent Japanese populations (1(st) population, 916 cases and 1,032 controls; 2(nd) population 1,034 cases and 1,004 controls). After the association results were combined by inverse variance method, we observed a significant association at rs4359426 (meta-analysis, combined P = 9.6×10⁻⁶; OR, 0.74; 95% CI, 0.65-0.85). Functional analysis revealed that the risk allele of rs4359426 contributed to higher expression levels of CCL22 mRNA. We further examined the allelic differences in the binding of nuclear proteins by electrophoretic mobility shift assay. The signal intensity of the DNA-protein complex derived from the G allele of rs223821, which was in absolute LD with rs4359426, was higher than that from the A allele. Although further functional analyses are needed, it is likely that related variants play a role in susceptibility to AD in a gain-of-function manner. Our findings provide a new insight into the etiology and pathogenesis of AD.

  5. Sequential motif profile of natural visibility graphs

    CERN Document Server

    Iacovacci, Jacopo

    2016-01-01

    The concept of sequential visibility graph motifs -subgraphs appearing with characteristic frequencies in the visibility graphs associated to time series- has been advanced recently along with a theoretical framework to compute analytically the motif profiles associated to Horizontal Visibility Graphs (HVGs). Here we develop a theory to compute the profile of sequential visibility graph motifs in the context of Natural Visibility Graphs (VGs). This theory gives exact results for deterministic aperiodic processes with a smooth invariant density or stochastic processes that fulfil the Markov property and have a continuous marginal distribution. The framework also allows for a linear time numerical estimation in the case of empirical time series. A comparison between the HVG and the VG case (including evaluation of their robustness for short series polluted with measurement noise) is also presented.

  6. Armadillo motifs involved in vesicular transport.

    Directory of Open Access Journals (Sweden)

    Harald Striegl

    Full Text Available Armadillo (ARM repeat proteins function in various cellular processes including vesicular transport and membrane tethering. They contain an imperfect repeating sequence motif that forms a conserved three-dimensional structure. Recently, structural and functional insight into tethering mediated by the ARM-repeat protein p115 has been provided. Here we describe the p115 ARM-motifs for reasons of clarity and nomenclature and show that both sequence and structure are highly conserved among ARM-repeat proteins. We argue that there is no need to invoke repeat types other than ARM repeats for a proper description of the structure of the p115 globular head region. Additionally, we propose to define a new subfamily of ARM-like proteins and show lack of evidence that the ARM motifs found in p115 are present in other long coiled-coil tethering factors of the golgin family.

  7. NCBI nr-aa BLAST: CBRC-PCAP-01-0571 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PCAP-01-0571 ref|NP_001001618.1| chemokine (C-C motif) receptor 5 [Sus scrofa]... dbj|BAD08649.1| chemokine (C-C motif) receptor 5 [Sus scrofa] dbj|BAD08656.1| chemokine (C-C motif) receptor 5 [Sus scrofa...] dbj|BAD12135.1| chemokine C-C motif eceptor 5 [Sus scrofa] NP_001001618.1 1e-168 79% ...

  8. NCBI nr-aa BLAST: CBRC-VPAC-01-1268 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-VPAC-01-1268 ref|NP_001001618.1| chemokine (C-C motif) receptor 5 [Sus scrofa]... dbj|BAD08649.1| chemokine (C-C motif) receptor 5 [Sus scrofa] dbj|BAD08656.1| chemokine (C-C motif) receptor 5 [Sus scrofa...] dbj|BAD12135.1| chemokine C-C motif eceptor 5 [Sus scrofa] NP_001001618.1 1e-151 76% ...

  9. NCBI nr-aa BLAST: CBRC-ETEL-01-0875 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-ETEL-01-0875 ref|NP_001001618.1| chemokine (C-C motif) receptor 5 [Sus scrofa]... dbj|BAD08649.1| chemokine (C-C motif) receptor 5 [Sus scrofa] dbj|BAD08656.1| chemokine (C-C motif) receptor 5 [Sus scrofa...] dbj|BAD12135.1| chemokine C-C motif eceptor 5 [Sus scrofa] NP_001001618.1 1e-155 74% ...

  10. NCBI nr-aa BLAST: CBRC-TGUT-04-0033 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-TGUT-04-0033 ref|NP_001001618.1| chemokine (C-C motif) receptor 5 [Sus scrofa]... dbj|BAD08649.1| chemokine (C-C motif) receptor 5 [Sus scrofa] dbj|BAD08656.1| chemokine (C-C motif) receptor 5 [Sus scrofa...] dbj|BAD12135.1| chemokine C-C motif eceptor 5 [Sus scrofa] NP_001001618.1 1e-128 62% ...

  11. NCBI nr-aa BLAST: CBRC-MEUG-01-0804 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-MEUG-01-0804 ref|NP_001001618.1| chemokine (C-C motif) receptor 5 [Sus scrofa]... dbj|BAD08649.1| chemokine (C-C motif) receptor 5 [Sus scrofa] dbj|BAD08656.1| chemokine (C-C motif) receptor 5 [Sus scrofa...] dbj|BAD12135.1| chemokine C-C motif eceptor 5 [Sus scrofa] NP_001001618.1 1e-159 77% ...

  12. Thermoelectric properties of SiC/C composites from wood charcoal by pulse current sintering

    NARCIS (Netherlands)

    Fujisawa, M; Hata, T; Bronsveld, P; Castro, [No Value; Tanaka, F; Kikuchi, H; Imamura, Y

    2005-01-01

    SiC/C composites were investigated by sintering a mix of wood charcoal and SiO2 powder (32-45 mu m) at 1400, 1600 and 1800 degrees C under N-2 atmosphere with a pulse current sintering method. Thermoelectric properties of SiC/C composites were investigated by measuring the Seebeck coefficient and th

  13. 76 FR 44800 - Election of Reduced Research Credit Under Section 280C(c)(3)

    Science.gov (United States)

    2011-07-27

    ... [TD 9539] RIN 1545-BI09 Election of Reduced Research Credit Under Section 280C(c)(3) AGENCY: Internal... dates of applicability, see Sec. 1.280C- 4(c). FOR FURTHER INFORMATION CONTACT: David Selig, (202) 622... research credit under section 280C(c)(3). On July 16, 2009, a notice of proposed rulemaking...

  14. Ablation Resistance of C/C Composites with Atmospheric Plasma-Sprayed W Coating

    Science.gov (United States)

    Zhou, Zhe; Wang, Yuan; Gong, Jieming; Ge, Yicheng; Peng, Ke; Ran, Liping; Yi, Maozhong

    2016-12-01

    To improve the ablation resistance of carbon/carbon (C/C) composites, tungsten (W) coating with thickness of 1.2 mm was applied by atmospheric plasma spraying. The antiablation property of the coated composites was evaluated by oxyacetylene flame ablation experiments. The phase composition of the coating was investigated by a combination of x-ray diffraction analysis and scanning electron microscopy with energy-dispersive x-ray spectroscopy analysis. The ablation resistance of the coated C/C substrates was compared with that of uncoated C/C composites and C/C-CuZr composites after ablation for 30 s. The properties of the coated C/C composites after ablation time of 10, 30, 60, 90, 120, and 180 s were further studied. The results indicated that the mass and linear ablation rates of the W-coated C/C composites were lower than those of uncoated C/C or C/C-CuZr composites after ablation for 30 s. The coating exhibited heat stability after 120 s of ablation, with mass loss and linear ablation rates of 7.39 × 10-3 g/s and 3.50 × 10-3 mm/s, respectively. However, the W coating became ineffective and failed after ablation for 180 s. Three ablation regions could be identified, in which the ablation mechanism of the coating changed from thermochemical to thermophysical erosion to mechanical scouring with increasing ablation time.

  15. High affinity recognition of a Phytophthora protein by Arabidopsis via an RGD motif.

    Science.gov (United States)

    Senchou, V; Weide, R; Carrasco, A; Bouyssou, H; Pont-Lezica, R; Govers, F; Canut, H

    2004-02-01

    The RGD tripeptide sequence, a cell adhesion motif present in several extracellular matrix proteins of mammalians, is involved in numerous plant processes. In plant-pathogen interactions, the RGD motif is believed to reduce plant defence responses by disrupting adhesions between the cell wall and plasma membrane. Photoaffinity cross-linking of [125I]-azido-RGD heptapeptide in the presence of purified plasma membrane vesicles of Arabidopsis thaliana led to label incorporation into a single protein with an apparent molecular mass of 80 kDa. Incorporation could be prevented by excess RGD peptides, but also by the IPI-O protein, an RGD-containing protein secreted by the oomycete plant pathogen Phytophthora infestans. Hydrophobic cluster analysis revealed that the RGD motif of IPI-O (positions 53-56) is readily accessible for interactions. Single amino acid mutations in the RGD motif in IPI-O (of Asp56 into Glu or Ala) resulted in the loss of protection of the 80-kDa protein from labelling. Thus, the interaction between the two proteins is mediated through RGD recognition and the 80-kDa RGD-binding protein has the characteristics of a receptor for IPI-O. The IPI-O protein also disrupted cell wall-plasma membrane adhesions in plasmolysed A. thaliana cells, whereas IPI-O proteins mutated in the RGD motif (D56A and D56E) did not.

  16. Proton stopping in C+C, d+C, C+Ta and d+Ta collisions at 4.2A GeV/c

    CERN Document Server

    Simic, L; Simic, Lj.

    1998-01-01

    The shape of proton rapidity distributions is analysed in terms of their Gaussian components, and the average rapidity loss is determined in order to estimate the amount of stopping in C+C, d+C, C+Ta and d+Ta collisions at 4.2A GeV/c. Three Gaussians correspond to the nuclear transparency and describe well all peripheral and also C+C central collisions. Two-component shape is obtained in case of d+C and C+Ta central collisions. Finally one Gaussian, found in d+Ta central collisions, corresponds to the full stopping. The calculated values of the average rapidity loss support the qualitative relationship between the number of Gaussian components and the corresponding stopping power. It is also observed, in central collisions, that the average rapidity loss increases with the ratio of the number of target and the number of projectile participants.

  17. 在MATLAB环境下创建C/C++外部应用程序的方法%The Method of Establishing C/C++ Exterior Application under MATLAB

    Institute of Scientific and Technical Information of China (English)

    刘东华

    2000-01-01

    介绍了利用MATLAB编译器和MATLAB的C/C++Math函数库以及C/C++编译器生成C/C++应用程序的优点及具体的编译链接流程,并通过实例分析了创建C/C++应用程序的方法.

  18. An excursion from normal to inverted C-C bonds shows a clear demarcation between covalent and charge-shift C-C bonds.

    Science.gov (United States)

    Shaik, Sason; Chen, Zhenhua; Wu, Wei; Stanger, Amnon; Danovich, David; Hiberty, Philippe C

    2009-10-19

    What is the nature of the C-C bond? Valence bond and electron density computations of 16 C-C bonds show two families of bonds that flesh out as a phase diagram. One family, involving ethane, cyclopropane and so forth, is typified by covalent C-C bonding wherein covalent spin-pairing accounts for most of the bond energy. The second family includes the inverted bridgehead bonds of small propellanes, where the bond is neither covalent nor ionic, but owes its existence to the resonance stabilization between the respective structures; hence a charge-shift (CS) bond. The dual family also emerges from calculated and experimental electron density properties. Covalent C-C bonds are characterized by negative Laplacians of the density, whereas CS-bonds display small or positive Laplacians. The positive Laplacian defines a region suffering from neighbouring repulsive interactions, which is precisely the case in the inverted bonding region. Such regions are rich in kinetic energy, and indeed the energy-density analysis reveals that CS-bonds are richer in kinetic energy than the covalent C-C bonds. The large covalent-ionic resonance energy is precisely the mechanism that lowers the kinetic energy in the bonding region and restores equilibrium bonding. Thus, different degrees of repulsive strain create two bonding families of the same chemical bond made from a single atomic constituent. It is further shown that the idea of repulsive strain is portable and can predict the properties of propellanes of various sizes and different wing substituents. Experimentally (M. Messerschmidt, S. Scheins, L. Bruberth, M. Patzel, G. Szeimies, C. Paulman, P. Luger, Angew. Chem. 2005, 117, 3993-3997; Angew. Chem. Int. Ed. 2005, 44, 3925-3928), the C-C bond families are beautifully represented in [1.1.1]propellane, where the inverted C-C is a CS-bond, while the wings are made from covalent C-C bonds. What other manifestations can we expect from CS-bonds? Answers from experiment have the potential

  19. Identifying motifs in folktales using topic models

    NARCIS (Netherlands)

    Karsdorp, F.; Bosch, A.P.J. van den

    2013-01-01

    With the undertake of various folktale digitalization initiatives, the need for computational aids to explore these collections is increasing. In this paper we compare Labeled LDA (L-LDA) to a simple retrieval model on the task of identifying motifs in folktales. We show that both methods are well a

  20. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  1. The Motif of Meeting in Digital Education

    Science.gov (United States)

    Sheail, Philippa

    2015-01-01

    This article draws on theoretical work which considers the composition of meetings, in order to think about the form of the meeting in digital environments for higher education. To explore the motif of meeting, I undertake a "compositional interpretation" (Rose, 2012) of the default interface offered by "Collaborate", an…

  2. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

  3. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun

    2013-06-29

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors\\' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  4. DNA motif elucidation using belief propagation.

    Science.gov (United States)

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-09-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.

  5. Microglial Immunoreceptor Tyrosine-Based Activation and Inhibition Motif Signaling in Neuroinflammation

    Directory of Open Access Journals (Sweden)

    Bettina Linnartz

    2010-01-01

    Full Text Available Elimination of extracellular aggregates and apoptotic neural membranes without inflammation is crucial for brain tissue homeostasis. In the mammalian central nervous system, essential molecules in this process are the Fc receptors and the DAP12-associated receptors which both trigger the microglial immunoreceptor tyrosine-based activation motif- (ITAM- Syk-signaling cascade. Microglial triggering receptor expressed on myeloid cells-2 (TREM2, signal regulatory protein-1, and complement receptor-3 (CD11b/CD18 signal via the adaptor protein DAP12 and activate phagocytic activity of microglia. Microglial ITAM-signaling receptors are counter-regulated by immunoreceptor tyrosine-based inhibition motif- (ITIM- signaling molecules such as sialic acid-binding immunoglobulin superfamily lectins (Siglecs. Siglecs can suppress the proinflammatory and phagocytic activity of microglia via ITIM signaling. Moreover, microglial neurotoxicity is alleviated via interaction of Siglec-11 with sialic acids on the neuronal glycocalyx. Thus, ITAM- and ITIM-signaling receptors modulate microglial phagocytosis and cytokine expression during neuroinflammatory processes. Their dysfunction could lead to impaired phagocytic clearance and neurodegeneration triggered by chronic inflammation.

  6. Effects of Hydrogen Ion Implantation on TiC-C Coating of Stainless Steel

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rui-qian; LIU Yao-guang; HUANG Ning-kang

    2008-01-01

    Titanium carbide coatings are widely used as various wear-resistant material.The hydrogen erosion resistance of TiC-C films and the effect of hydrogen participation on TiC-C films were studied.Seventy-five percent TiC-C films are prepared on stainless steel surface by using ion mixing,where TiC-C films are deposited by rf magnetron sputtering followed by argon ion bombardment.The samples are then submitted to hydrogen ion implantation at 1.2×10-3 Pa.Characterization for the 75% TiC-C films was done with SIMS,XRD,AES,and XPS.Secondary ion mass spectroscopy (SIMS) was used to analyze hydrogen concentration variation with depth,X-Ray diffraction (XRD) was used to identify the phases,and Auger electron spectra (AES) as well as X-ray photoelectron spectra (XPS) were used to check the effects of hydrogen on shifts of chemical bonding states of C and Ti in the TiC-C films.It is found that TiC-C films on stainless steel surface can prevent hydrogen from entering stainless steel.

  7. A discriminative approach for unsupervised clustering of DNA sequence motifs.

    Directory of Open Access Journals (Sweden)

    Philip Stegmaier

    Full Text Available Algorithmic comparison of DNA sequence motifs is a problem in bioinformatics that has received increased attention during the last years. Its main applications concern characterization of potentially novel motifs and clustering of a motif collection in order to remove redundancy. Despite growing interest in motif clustering, the question which motif clusters to aim at has so far not been systematically addressed. Here we analyzed motif similarities in a comprehensive set of vertebrate transcription factor classes. For this we developed enhanced similarity scores by inclusion of the information coverage (IC criterion, which evaluates the fraction of information an alignment covers in aligned motifs. A network-based method enabled us to identify motif clusters with high correspondence to DNA-binding domain phylogenies and prior experimental findings. Based on this analysis we derived a set of motif families representing distinct binding specificities. These motif families were used to train a classifier which was further integrated into a novel algorithm for unsupervised motif clustering. Application of the new algorithm demonstrated its superiority to previously published methods and its ability to reproduce entrained motif families. As a result, our work proposes a probabilistic approach to decide whether two motifs represent common or distinct binding specificities.

  8. Role of PY Motif Containing Protein, WBP-2 in ER, PR Signaling and Breast Tumorigenesis

    Science.gov (United States)

    2009-09-01

    and expression of the endogenous estrogen-regulated gene, pS2 were measured by real time polymerase chain reaction (RT-PCR). The siWBP-2...amplified by polymerase chain reaction (PCR) using pri- mers specific for estrogen receptor binding site within the pS2 promoter. ChIP analyses demonstrated...WW-domains and PPXY motif have been implicated in many diseases , including muscular dystrophy, Liddle’s syndrome, Alzheimer’s, Huntington disease

  9. Electron attachment properties of c-C4F8O in different environments

    Science.gov (United States)

    Chachereau, A.; Fedor, J.; Janečková, R.; Kočišek, J.; Rabie, M.; Franck, C. M.

    2016-09-01

    The electron attachment properties of octafluorotetrahydrofuran (c-C4F8O) are investigated using two complementary experimental setups. The attachment and ionization cross sections of c-C4F8O are measured using an electron beam experiment. The effective ionization rate coefficient, electron drift velocity and electron diffusion coefficient in c-C4F8O diluted to concentrations lower than 0.6% in the buffer gases N2, CO2 and Ar, are measured using a pulsed Townsend experiment. A kinetic model is proposed, which combines the results of the two experiments.

  10. Using SCOPE to identify potential regulatory motifs in coregulated genes.

    Science.gov (United States)

    Martyanov, Viktor; Gross, Robert H

    2011-05-31

    SCOPE is an ensemble motif finder that uses three component algorithms in parallel to identify potential regulatory motifs by over-representation and motif position preference. Each component algorithm is optimized to find a different kind of motif. By taking the best of these three approaches, SCOPE performs better than any single algorithm, even in the presence of noisy data. In this article, we utilize a web version of SCOPE to examine genes that are involved in telomere maintenance. SCOPE has been incorporated into at least two other motif finding programs and has been used in other studies. The three algorithms that comprise SCOPE are BEAM, which finds non-degenerate motifs (ACCGGT), PRISM, which finds degenerate motifs (ASCGWT), and SPACER, which finds longer bipartite motifs (ACCnnnnnnnnGGT). These three algorithms have been optimized to find their corresponding type of motif. Together, they allow SCOPE to perform extremely well. Once a gene set has been analyzed and candidate motifs identified, SCOPE can look for other genes that contain the motif which, when added to the original set, will improve the motif score. This can occur through over-representation or motif position preference. Working with partial gene sets that have biologically verified transcription factor binding sites, SCOPE was able to identify most of the rest of the genes also regulated by the given transcription factor. Output from SCOPE shows candidate motifs, their significance, and other information both as a table and as a graphical motif map. FAQs and video tutorials are available at the SCOPE web site which also includes a "Sample Search" button that allows the user to perform a trial run. Scope has a very friendly user interface that enables novice users to access the algorithm's full power without having to become an expert in the bioinformatics of motif finding. As input, SCOPE can take a list of genes, or FASTA sequences. These can be entered in browser text fields, or read from

  11. Bases of motifs for generating repeated patterns with wild cards

    OpenAIRE

    Pisanti, Nadia; Crochemore, Maxime; Grossi, Roberto; Sagot, Marie-France

    2005-01-01

    Motif inference represents one of the most important areas of research in computational biology, and one of its oldest ones. Despite this, the problem remains very much open in the sense that no existing definition is fully satisfying, either in formal terms, or in relation to the biological questions that involve finding such motifs. Two main types of motifs have been considered in the literature: matrices (of letter frequency per position in the motif) and patterns. There is no conclusive e...

  12. Manganese(I)-Catalyzed Dispersion-Enabled C-H/C-C Activation.

    Science.gov (United States)

    Meyer, Tjark H; Liu, Weiping; Feldt, Milica; Wuttke, Axel; Mata, Ricardo A; Ackermann, Lutz

    2017-03-20

    C-H/C-C Functionalizations were achieved with the aid of a versatile manganese(I) catalyst. Thus, an organometallic manganese-catalyzed C-H activation set the stage for silver-free C-H/C-C transformations with ample substrate scope and excellent levels of chemo-, site-, and diastereo-selectivities. The robust nature of the manganese(I) catalysis regime was reflected by the first C-H/C-C functionalization on amino acids under racemization-free reaction conditions. Detailed experimental and computational mechanistic studies provided strong evidence for a facile C-H activation and a rate-determining C-C cleavage, with considerable contribution from London dispersion interactions.

  13. Mathematical Simulation of Graphene With Modified c-c Bond Length and Transfer Energy

    Directory of Open Access Journals (Sweden)

    P.A. Alvi

    2011-01-01

    Full Text Available In nanotechnology research, allotropes of carbon like Graphene, Fullerene (Buckyball and Carbon nanotubes are widely used due to their remarkable properties. Electrical and mechanical properties of those allotropes vary with their molecular geometry. This paper is specially based on modeling and simulation of graphene in order to calculate energy band structure in k space with varying the C-C bond length and C-C transfer energy. Significant changes have been observed in the energy band structure of graphene due to variation in C-C bond length and C-C transfer energy. In particular, this paper focuses over the electronic structure of graphene within the frame work of tight binding approximation. It has been reported that conduction and valence states in graphene only meet at two points in k-space and that dispersion around these special points is conical.

  14. Observation of the decay $\\psi(3686)$ $\\rightarrow$ $\\Lambda\\bar\\Sigma^{\\pm}\\pi^{\\mp}+c.c.$

    CERN Document Server

    Ablikim, M; Ai, X C; Albayrak, O; Ambrose, D J; An, F F; An, Q; Bai, J Z; A, R Baldini Ferroli; Ban, Y; Bennett, J V; A, M Bertani; Bian, J M; Boger, E; Bondarenko, O; Boyko, I; Braun, S; Briere, R A; Cai, H; Cai, X; A, O Cakir; A, A Calcaterra; Cao, G F; B, S A Cetin; Chang, J F; Chelkov, G; Chen, G; Chen, H S; Chen, J C; Chen, M L; Chen, S J; Chen, X; Chen, X R; Chen, Y B; Cheng, H P; Chu, X K; Chu, Y P; Cronin-Hennessy, D; Dai, H L; Dai, J P; Dedovich, D; Deng, Z Y; Denig, A; Denysenko, I; Destefanis, M; Ding, W M; Ding, Y; Dong, C; Dong, J; Dong, L Y; Dong, M Y; Du, S X; Fang, J; Fang, S S; Fang, Y; Fava, L; Feng, C Q; Fu, C D; Fu, J L; Fuks, O; Gao, Q; Gao, Y; Geng, C; Goetzen, K; Gong, W X; Gradl, W; Greco, M; Gu, M H; Gu, Y T; Guan, Y H; Guo, A Q; Guo, L B; Guo, T; Guo, Y P; Han, Y L; Harris, F A; He, K L; He, M; He, Z Y; Held, T; Heng, Y K; Hou, Z L; Hu, C; Hu, H M; Hu, J F; Hu, T; Huang, G M; Huang, G S; Huang, J S; Huang, L; Huang, X T; Hussain, T; Ji, C S; Ji, Q; Ji, Q P; Ji, X B; Ji, X L; Jiang, L L; Jiang, X S; Jiao, J B; Jiao, Z; Jin, D P; Jin, S; Jing, F F; Johansson, T; Kalantar-Nayestanaki, N; Kang, X L; Kavatsyuk, M; Kloss, B; Kopf, B; Kornicer, M; Kuehn, W; Kupsc, A; Lai, W; Lange, J S; Lara, M; Larin, P; Leyhe, M; Li, C H; Li, Cheng; Li, Cui; Li, D; Li, D M; Li, F; Li, G; Li, H B; Li, J C; Li, K; Li, Lei; Li, P R; Li, Q J; Li, T; Li, W D; Li, W G; Li, X L; Li, X N; Li, X Q; Li, X R; Li, Z B; Liang, H; Liang, Y F; Liang, Y T; Liao, G R; Lin, D X; Liu, B J; Liu, C L; Liu, C X; Liu, F H; Liu, Fang; Liu, Feng; Liu, H B; Liu, H H; Liu, H M; Liu, J; Liu, J P; Liu, K; Liu, K Y; Liu, P L; Liu, Q; Liu, S B; Liu, X; Liu, Y B; Liu, Z A; Liu, Zhiqiang; Liu, Zhiqing; Loehner, H; Lou, X C; Lu, G R; Lu, H J; Lu, H L; Lu, J G; Lu, X R; Lu, Y; Lu, Y P; Luo, C L; Luo, M X; Luo, T; Luo, X L; Lv, M; Ma, F C; Ma, H L; Ma, Q M; Ma, S; Ma, T; Ma, X Y; Maas, F E; Maggiora, M; Malik, Q A; Mao, Y J; Mao, Z P; Messchendorp, J G; Min, J; Min, T J; Mitchell, R E; Mo, X H; Moeini, H; Morales, C Morales; Moriya, K; Muchnoi, N Yu; Nefedov, Y; Nikolaev, I B; Ning, Z; Nisar, S; Niu, X Y; Olsen, S L; Ouyang, Q; B, S Pacetti; Pelizaeus, M; Peng, H P; Peters, K; Ping, J L; Ping, R G; Poling, R; Prencipe, E; Qi, M; Qian, S; Qiao, C F; Qin, L Q; Qin, X S; Qin, Y; Qin, Z H; Qiu, J F; Rashid, K H; Redmer, C F; Ripka, M; Rong, G; Ruan, X D; Sarantsev, A; Schinning, K; Schumann, S; Shan, W; Shao, M; Shen, C P; Shen, X Y; Sheng, H Y; Shepherd, M R; Song, W M; Song, X Y; Spataro, S; Spruck, B; Sun, G X; Sun, J F; Sun, S S; Sun, Y J; Sun, Y Z; Sun, Z J; Sun, Z T; Tang, C J; Tang, X; Tapan, I; Thorndike, E H; Toth, D; Ullrich, M; B, I Uman; Varner, G S; Wang, B; Wang, D; Wang, D Y; Wang, K; Wang, L L; Wang, L S; Wang, M; Wang, P; Wang, P L; Wang, Q J; Wang, S G; Wang, W; Wang, X F; A, Y D Wang; Wang, Y F; Wang, Y Q; Wang, Z; Wang, Z G; Wang, Z H; Wang, Z Y; Wei, D H; Wei, J B; Weidenkaff, P; Wen, S P; Werner, M; Wiedner, U; Wolke, M; Wu, G G; Wu, L H; Wu, N; Wu, W; Wu, Z; Xia, L G; Xia, Y; Xiao, D; Xiao, Z J; Xie, Y G; Xiu, Q L; Xu, G F; Xu, L; Xu, Q J; Xu, Q N; Xu, X P; Xue, Z; Yan, L; Yan, W B; Yan, W C; Yan, Y H; Yang, H X; Yang, Y; Yang, Y X; Ye, H; Ye, M; Ye, M H; Yu, B X; Yu, C X; Yu, H W; Yu, J S; Yu, S P; Yuan, C Z; Yuan, W L; Yuan, Y; Zafar, A A; A, A Zallo; Zang, S L; Zeng, Y; Zhang, B X; Zhang, B Y; Zhang, C; Zhang, C B; Zhang, C C; Zhang, D H; Zhang, H H; Zhang, H Y; Zhang, J J; Zhang, J L; Zhang, J Q; Zhang, J W; Zhang, J Y; Zhang, J Z; Zhang, S H; Zhang, X J; Zhang, X Y; Zhang, Y; Zhang, Y H; Zhang, Z H; Zhang, Z P; Zhang, Z Y; Zhao, G; Zhao, J W; Zhao, Lei; Zhao, Ling; Zhao, M G; Zhao, Q; Zhao, Q W; Zhao, S J; Zhao, T C; Zhao, X H; Zhao, Y B; Zhao, Z G; Zhemchugov, A; Zheng, B; Zheng, J P; Zheng, Y H; Zhong, B; Zhou, L; Zhou, Li; Zhou, X; Zhou, X K; Zhou, X R; Zhou, X Y; Zhu, K; Zhu, K J; Zhu, X L; Zhu, Y C; Zhu, Y S; Zhu, Z A; Zhuang, J; Zou, B S; Zou, J H

    2013-01-01

    Using a sample of $1.06\\times10^{8}$ $\\psi(3686)$ events collected with the BESIII detector, we present the first observation of the decays of $\\psi(3686)$ $\\rightarrow$ $\\Lambda\\bar\\Sigma^{+}\\pi^{-}+c.c.$ and $\\psi(3686)$ $\\rightarrow$ $\\Lambda\\bar\\Sigma^{-}\\pi^{+}+c.c.$. The branching fractions are measured to be $\\mathcal{B}(\\psi(3686) \\rightarrow \\Lambda\\bar\\Sigma^{+}\\pi^{-} + c.c.)=(1.40\\pm 0.03 \\pm 0.13)\\times10^{-4}$ and $\\mathcal{B}(\\psi(3686) \\rightarrow \\Lambda\\bar\\Sigma^{-}\\pi^{+}+c.c.)=(1.54\\pm 0.04 \\pm 0.13)\\times10^{-4}$, where the first errors are statistical and the second ones systematic.

  15. Anticipated synchronization in neuronal network motifs

    Science.gov (United States)

    Matias, F. S.; Gollo, L. L.; Carelli, P. V.; Copelli, M.; Mirasso, C. R.

    2013-01-01

    Two identical dynamical systems coupled unidirectionally (in a so called master-slave configuration) exhibit anticipated synchronization (AS) if the one which receives the coupling (the slave) also receives a negative delayed self-feedback. In oscillatory neuronal systems AS is characterized by a phase-locking with negative time delay τ between the spikes of the master and of the slave (slave fires before the master), while in the usual delayed synchronization (DS) regime τ is positive (slave fires after the master). A 3-neuron motif in which the slave self-feedback is replaced by a feedback loop mediated by an interneuron can exhibits both AS and DS regimes. Here we show that AS is robust in the presence of noise in a 3 Hodgkin-Huxley type neuronal motif. We also show that AS is stable for large values of τ in a chain of connected slaves-interneurons.

  16. Chiral Alkyl Halides: Underexplored Motifs in Medicine

    Directory of Open Access Journals (Sweden)

    Bálint Gál

    2016-11-01

    Full Text Available While alkyl halides are valuable intermediates in synthetic organic chemistry, their use as bioactive motifs in drug discovery and medicinal chemistry is rare in comparison. This is likely attributable to the common misconception that these compounds are merely non-specific alkylators in biological systems. A number of chlorinated compounds in the pharmaceutical and food industries, as well as a growing number of halogenated marine natural products showing unique bioactivity, illustrate the role that chiral alkyl halides can play in drug discovery. Through a series of case studies, we demonstrate in this review that these motifs can indeed be stable under physiological conditions, and that halogenation can enhance bioactivity through both steric and electronic effects. Our hope is that, by placing such compounds in the minds of the chemical community, they may gain more traction in drug discovery and inspire more synthetic chemists to develop methods for selective halogenation.

  17. Type 2 diabetes mellitus: phylogenetic motifs for predicting protein functional sites

    Indian Academy of Sciences (India)

    Ashok Sharma; Tanuja Rastogi; Meenakshi Bhartiya; A K Shasany; S P S Khanuja

    2007-08-01

    Diabetes mellitus, commonly referred to as diabetes, is a medical condition associated with abnormally high levels of glucose (or sugar) in the blood. Keeping this view, we demonstrate the phylogenetic motifs (PMs) identification in type 2 diabetes mellitus very likely corresponding to protein functional sites. In this article, we have identified PMs for all the candidate genes for type 2 diabetes mellitus. Glycine 310 remains conserved for glucokinase and potassium channel KCNJ11. Isoleucine 137 was conserved for insulin receptor and regulatory subunit of a phosphorylating enzyme. Whereas residues valine, leucine, methionine were highly conserved for insulin receptor. Occurrence of proline was very high for calpain 10 gene and glucose transporter

  18. Photocatalytic C-C Bond Cleavage and Amination of Cycloalkanols by Cerium(III) Chloride Complex.

    Science.gov (United States)

    Guo, Jing-Jing; Hu, Anhua; Chen, Yilin; Sun, Jianfeng; Tang, Haoming; Zuo, Zhiwei

    2016-12-05

    A general strategy for the cleavage and amination of C-C bonds of cycloalkanols has been achieved through visible-light-induced photoredox catalysis utilizing a cerium(III) chloride complex. This operationally simple methodology has been successfully applied to a wide array of unstrained cyclic alcohols, and represents the first example of catalytic C-C bond cleavage and functionalization of unstrained secondary cycloalkanols.

  19. Mathematical Simulation of Graphene With Modified c-c Bond Length and Transfer Energy

    OpenAIRE

    P.A. Alvi; S.Z. Hashmi; S. Dalela; Rahman, F.

    2011-01-01

    In nanotechnology research, allotropes of carbon like Graphene, Fullerene (Buckyball) and Carbon nanotubes are widely used due to their remarkable properties. Electrical and mechanical properties of those allotropes vary with their molecular geometry. This paper is specially based on modeling and simulation of graphene in order to calculate energy band structure in k space with varying the C-C bond length and C-C transfer energy. Significant changes have been observed in the energy band struc...

  20. MINER: software for phylogenetic motif identification

    OpenAIRE

    La, David; Livesay, Dennis R.

    2005-01-01

    MINER is web-based software for phylogenetic motif (PM) identification. PMs are sequence regions (fragments) that conserve the overall familial phylogeny. PMs have been shown to correspond to a wide variety of catalytic regions, substrate-binding sites and protein interfaces, making them ideal functional site predictions. The MINER output provides an intuitive interface for interactive PM sequence analysis and structural visualization. The web implementation of MINER is freely available at . ...

  1. MENGUNGKAP SEJARAH DAN MOTIF BATIK SEMARANGAN

    Directory of Open Access Journals (Sweden)

    Dewi Yuliati

    2011-10-01

    Full Text Available Batik Semarang was born in line with the needs of the people of Hyderabad of the material with a new motif or style tailored to the taste, intention, and creativity of the craftsmen. Batik is a combination of several countries influence developing in Indonesian culture. Based on its shape, Batik designs can be divided into two major groups, namely geometric and non-Geometric. The development of Semarangan batik was due to the fact that certain motif of batik can only be worn by certain people, not for all group of people. Batik semarangan craftments are found in coastal regions. It displays the design composing of ornaments plucked from marine environment. Indonesian Batik develops not only to display a blending of court Batik designs with the coastal Batik technique, but also to incorporate other ornaments which come from many various ethnic groups in Indonesia.   Key words: batik, history, ornaments, marine environment, designs   Batik Semarang lahirkan sejalan dengan kebutuhan dari orang-orang dari Hyderabad akan bahan dengan motif atau gaya baru yang berdasarkan pada rasa, niat, dan kreatifitas dari pembuatnya. Batik merupakan perpaduan dari pengaruh beberapa negara yang berkembang dalam budaya Indonesia. Ditinjau dari desainnya, desain batik dapat dibagi menjadi dua kelompok utama, yakni geometrik dan nongeometrik. Pengembangan yang dilakukan terhadap batik semarangan disebabkan adanya beberapa motif batik yang hanya digunakan oleh kalangan tertentu, dan tidak boleh untuk kalangan umum. Pengrajin batik Semarangan berkembang di kawasan pesisir. Ia menampilkan desain yang terdiri atas berbagai ornamen yang menunjukkan ciri khas kemaritiman. Batik ini dikembangakan tidak hanya menampilkan desain batik khas pesisiran, tetapi juga memasukkan berbagai ornament dari beragam kelompok etnis di Indonesia.   Kata kunci: batik, sejarah, ragam hias, lingkungan pesisir, desain  

  2. Social Network Analysis Based on Network Motifs

    OpenAIRE

    2014-01-01

    Based on the community structure characteristics, theory, and methods of frequent subgraph mining, network motifs findings are firstly introduced into social network analysis; the tendentiousness evaluation function and the importance evaluation function are proposed for effectiveness assessment. Compared with the traditional way based on nodes centrality degree, the new approach can be used to analyze the properties of social network more fully and judge the roles of the nodes effectively. I...

  3. Trading networks, abnormal motifs and stock manipulation

    OpenAIRE

    2012-01-01

    We study trade-based manipulation of stock prices from the perspective of complex trading networks constructed by using detailed information of trades. A stock trading network consists of nodes and directed links, where every trader is a node and a link is formed from one trader to the other if the former sells shares to the latter. Specifically, three abnormal network motifs are investigated, which are found to be formed by a few traders, implying potential intention of price manipulation. W...

  4. Evaluation by Rocket Combustor of C/C Composite Cooled Structure Using Metallic Cooling Tubes

    Science.gov (United States)

    Takegoshi, Masao; Ono, Fumiei; Ueda, Shuichi; Saito, Toshihito; Hayasaka, Osamu

    In this study, the cooling performance of a C/C composite material structure with metallic cooling tubes fixed by elastic force without chemical bonding was evaluated experimentally using combustion gas in a rocket combustor. The C/C composite chamber was covered by a stainless steel outer shell to maintain its airtightness. Gaseous hydrogen as a fuel and gaseous oxygen as an oxidizer were used for the heating test. The surface of these C/C composites was maintained below 1500 K when the combustion gas temperature was about 2800 K and the heat flux to the combustion chamber wall was about 9 MW/m2. No thermal damage was observed on the stainless steel tubes that were in contact with the C/C composite materials. The results of the heating test showed that such a metallic tube-cooled C/C composite structure is able to control the surface temperature as a cooling structure (also as a heat exchanger) as well as indicated the possibility of reducing the amount of coolant even if the thermal load to the engine is high. Thus, application of this metallic tube-cooled C/C composite structure to reusable engines such as a rocket-ramjet combined-cycle engine is expected.

  5. Dynamic motifs in socio-economic networks

    Science.gov (United States)

    Zhang, Xin; Shao, Shuai; Stanley, H. Eugene; Havlin, Shlomo

    2014-12-01

    Socio-economic networks are of central importance in economic life. We develop a method of identifying and studying motifs in socio-economic networks by focusing on “dynamic motifs,” i.e., evolutionary connection patterns that, because of “node acquaintances” in the network, occur much more frequently than random patterns. We examine two evolving bi-partite networks: i) the world-wide commercial ship chartering market and ii) the ship build-to-order market. We find similar dynamic motifs in both bipartite networks, even though they describe different economic activities. We also find that “influence” and “persistence” are strong factors in the interaction behavior of organizations. When two companies are doing business with the same customer, it is highly probable that another customer who currently only has business relationship with one of these two companies, will become customer of the second in the future. This is the effect of influence. Persistence means that companies with close business ties to customers tend to maintain their relationships over a long period of time.

  6. Multilayer motif analysis of brain networks

    CERN Document Server

    Battiston, Federico; Chavez, Mario; Latora, Vito

    2016-01-01

    In the last decade network science has shed new light on the anatomical connectivity and on correlations in the activity of different areas of the human brain. The study of brain networks has made possible in fact to detect the central areas of a neural system, and to identify its building blocks by looking at overabundant small subgraphs, known as motifs. However, network analysis of the brain has so far mainly focused on structural and functional networks as separate entities. The recently developed mathematical framework of multi-layer networks allows to perform a multiplex analysis of the human brain where the structural and functional layers are considered at the same time. In this work we describe how to classify subgraphs in multiplex networks, and we extend motif analysis to networks with many layers. We then extract multi-layer motifs in brain networks of healthy subjects by considering networks with two layers, respectively obtained from diffusion and functional magnetic resonance imaging. Results i...

  7. Linux平台C/C++和汇编昆合编程%C/C++ Language and Assemble Language Combination Programming Based on Linux

    Institute of Scientific and Technical Information of China (English)

    郝丽花; 张世禄; 张杨军

    2004-01-01

    Linux的核心代码大部分是用C语言编写的,不可避免的其中还有一部分是用汇编语言写成的.有些汇编语言代码是利用gcc的内嵌语句直接嵌在C语言程序中的;还有一些则是写在汇编源程序中的,特别是Linux的启动代码部分.文章介绍了在Linux的gcc/g++环境下,C/C++程序中如何内嵌汇编代码;分析了汇编源程序如何与调用它的C/C++程序接口.

  8. 使用Visual Leak Detector检测c/c++程序内存泄漏%Memory Leak Detection in c/c++ Programs with Visual Leak Detector

    Institute of Scientific and Technical Information of China (English)

    杨磊; 汪仁煌; 刘洪江; 黄颖怡

    2008-01-01

    针对内存泄漏检测问题,本文通过示例说明使用软件Visual Leal Detector 来检测泄漏点的方法.通过实验说明该方法在检测一般的c/c++程序内存泄漏时,可以提高检测效率.

  9. The interface between C/C++ and assembler in gcc/g++%gcc/g++下C/C++和汇编的接口

    Institute of Scientific and Technical Information of China (English)

    陈付龙; 汪迅宝; 李明东

    2004-01-01

    汇编语言是低级语言,与硬件和操作系统紧密联系.它能够完成许多其他语言所不能完成的功能.笔者较详细地分析了在Linux平台的gcc/g++开发环境下,汇编程序与调用它的C/C++程序的接口约定.

  10. Large-scale discovery of promoter motifs in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Thomas A Down

    2007-01-01

    Full Text Available A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.

  11. ET-Motif: Solving the Exact (l, d)-Planted Motif Problem Using Error Tree Structure.

    Science.gov (United States)

    Al-Okaily, Anas; Huang, Chun-Hsi

    2016-07-01

    Motif finding is an important and a challenging problem in many biological applications such as discovering promoters, enhancers, locus control regions, transcription factors, and more. The (l, d)-planted motif search, PMS, is one of several variations of the problem. In this problem, there are n given sequences over alphabets of size [Formula: see text], each of length m, and two given integers l and d. The problem is to find a motif m of length l, where in each sequence there is at least an l-mer at a Hamming distance of [Formula: see text] of m. In this article, we propose ET-Motif, an algorithm that can solve the PMS problem in [Formula: see text] time and [Formula: see text] space. The time bound can be further reduced by a factor of m with [Formula: see text] space. In case the suffix tree that is built for the input sequences is balanced, the problem can be solved in [Formula: see text] time and [Formula: see text] space. Similarly, the time bound can be reduced by a factor of m using [Formula: see text] space. Moreover, the variations of the problem, namely the edit distance PMS and edited PMS (Quorum), can be solved using ET-Motif with simple modifications but upper bands of space and time. For edit distance PMS, the time and space bounds will be increased by [Formula: see text], while for edited PMS the increase will be of [Formula: see text] in the time bound.

  12. Identification of a binding element for the cytoplasmic regulator FROUNT in the membrane-proximal C-terminal region of chemokine receptors CCR2 and CCR5.

    Science.gov (United States)

    Toda, Etsuko; Terashima, Yuya; Esaki, Kaori; Yoshinaga, Sosuke; Sugihara, Minoru; Kofuku, Yutaka; Shimada, Ichio; Suwa, Makiko; Kanegasaki, Shiro; Terasawa, Hiroaki; Matsushima, Kouji

    2014-01-15

    Chemokine receptors mediate the migration of leucocytes during inflammation. The cytoplasmic protein FROUNT binds to chemokine receptors CCR2 [chemokine (C-C motif) receptor 2] and CCR5, and amplifies chemotactic signals in leucocytes. Although the interaction between FROUNT and chemokine receptors is important for accurate chemotaxis, the interaction mechanism has not been elucidated. In the present study we identified a 16-amino-acid sequence responsible for high-affinity binding of FROUNT at the membrane-proximal C-terminal intracellular region of CCR2 (CCR2 Pro-C) by yeast two-hybrid analysis. Synthesized peptides corresponding to the CCR2 Pro-C sequence directly interacted with FROUNT in vitro. CCR2 Pro-C was predicted to form an amphipathic helix structure. Residues on the hydrophobic side are completely conserved among FROUNT-binding receptors, suggesting that the hydrophobic side is the responsible element for FROUNT binding. The L316T mutation to the hydrophobic side of the predicted helix decreased the affinity for FROUNT. Co-immunoprecipitation assays revealed that the CCR2 L316T mutation diminished the interaction between FROUNT and full-length CCR2 in cells. Furthermore, this mutation impaired the ability of the receptor to mediate chemotaxis. These findings provide the first description of the functional binding element in helix 8 of CCR2 for the cytosolic regulator FROUNT that mediates chemotactic signalling.

  13. The cysteine-cluster motif of c-Yes, Lyn and FAK as a suppressive module for the kinases.

    Science.gov (United States)

    Rahman, Mohammad Aminur; Senga, Takeshi; Oo, Myat Lin; Hasegawa, Hitoki; Biswas, Md Helal Uddin; Mon, Naing Naing; Huang, Pengyu; Ito, Satoko; Yamamoto, Tadashi; Hamaguchi, Michinari

    2008-04-01

    The Src family of non-receptor protein tyrosine kinases plays a critical role in the progression of human cancers so that the development of its specific inhibitors is important as a therapeutic tool. We previously reported that cysteine residues in the cysteine-cluster (CC) motif of v-Src were critical for the kinase inactivation by the SH-alkylating agents such as N-(9-acridinyl) maleimide (NAM), whereas other cysteine residues were dispensable. We found similar CC-motifs in other Src-family kinases and a non-Src-family kinase, FAK. In this study, we explored the function of the CC-motif in Yes, Lyn and FAK. While Src has four cysteines in the CC-motif, c-Yes and Lyn have three and two of the four cysteines, respectively. Two conserved cysteines of the Src family kinases, corresponding to Cys487 and Cys498 of Src, were essential for the resistance to the inactivation of the kinase activity by NAM, whereas the first cysteine of c-Yes, which is absent in Lyn, was less important. FAK has similar CC-motifs with two cysteines and both cysteines were again essential for the resistance to the inactivation of the kinase activity by NAM. Taken together, modification of cysteine residues of the CC-motif causes a repressor effect on the catalytic activity of the Src family kinases and FAK.

  14. Dynamics of network motifs in genetic regulatory networks

    Institute of Scientific and Technical Information of China (English)

    Li Ying; Liu Zeng-Rong; Zhang Jian-Bao

    2007-01-01

    Network motifs hold a very important status in genetic regulatory networks. This paper aims to analyse the dynamical property of the network motifs in genetic regulatory networks. The main result we obtained is that the dynamical property of a single motif is very simple with only an asymptotically stable equilibrium point, but the combination of several motifs can make more complicated dynamical properties emerge such as limit cycles. The above-mentioned result shows that network motif is a stable substructure in genetic regulatory networks while their combinations make the genetic regulatory network more complicated.

  15. No tradeoff between versatility and robustness in gene circuit motifs

    Science.gov (United States)

    Payne, Joshua L.

    2016-05-01

    Circuit motifs are small directed subgraphs that appear in real-world networks significantly more often than in randomized networks. In the Boolean model of gene circuits, most motifs are realized by multiple circuit genotypes. Each of a motif's constituent circuit genotypes may have one or more functions, which are embodied in the expression patterns the circuit forms in response to specific initial conditions. Recent enumeration of a space of nearly 17 million three-gene circuit genotypes revealed that all circuit motifs have more than one function, with the number of functions per motif ranging from 12 to nearly 30,000. This indicates that some motifs are more functionally versatile than others. However, the individual circuit genotypes that constitute each motif are less robust to mutation if they have many functions, hinting that functionally versatile motifs may be less robust to mutation than motifs with few functions. Here, I explore the relationship between versatility and robustness in circuit motifs, demonstrating that functionally versatile motifs are robust to mutation despite the inherent tradeoff between versatility and robustness at the level of an individual circuit genotype.

  16. CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design.

    Science.gov (United States)

    Zhang, Shaoqiang; Chen, Yong

    2016-01-01

    A set of conserved binding sites recognized by a transcription factor is called a motif, which can be found by many applications of comparative genomics for identifying over-represented segments. Moreover, when numerous putative motifs are predicted from a collection of genome-wide data, their similarity data can be represented as a large graph, where these motifs are connected to one another. However, an efficient clustering algorithm is desired for clustering the motifs that belong to the same groups and separating the motifs that belong to different groups, or even deleting an amount of spurious ones. In this work, a new motif clustering algorithm, CLIMP, is proposed by using maximal cliques and sped up by parallelizing its program. When a synthetic motif dataset from the database JASPAR, a set of putative motifs from a phylogenetic foot-printing dataset, and a set of putative motifs from a ChIP dataset are used to compare the performances of CLIMP and two other high-performance algorithms, the results demonstrate that CLIMP mostly outperforms the two algorithms on the three datasets for motif clustering, so that it can be a useful complement of the clustering procedures in some genome-wide motif prediction pipelines. CLIMP is available at http://sqzhang.cn/climp.html.

  17. RNA structural motif recognition based on least-squares distance.

    Science.gov (United States)

    Shen, Ying; Wong, Hau-San; Zhang, Shaohong; Zhang, Lin

    2013-09-01

    RNA structural motifs are recurrent structural elements occurring in RNA molecules. RNA structural motif recognition aims to find RNA substructures that are similar to a query motif, and it is important for RNA structure analysis and RNA function prediction. In view of this, we propose a new method known as RNA Structural Motif Recognition based on Least-Squares distance (LS-RSMR) to effectively recognize RNA structural motifs. A test set consisting of five types of RNA structural motifs occurring in Escherichia coli ribosomal RNA is compiled by us. Experiments are conducted for recognizing these five types of motifs. The experimental results fully reveal the superiority of the proposed LS-RSMR compared with four other state-of-the-art methods.

  18. CONTEMPORARY USAGE OF TRADITIONAL TURKISH MOTIFS IN PRODUCT DESIGNS

    Directory of Open Access Journals (Sweden)

    Tulay Gumuser

    2012-12-01

    Full Text Available The aim of this study is to identify the traditional Turkish motifs and its relations among present industrial designs. Traditional Turkish motifs played a very important role in 16th century onwards. The arts of the Ottoman Empire were used because of their symbolic meanings and unique styles. When we examine these motifs we encounter; Tiger Stripe, Three Spot (Çintemani, Rumi, Hatayi, Penç, Cloud, Crescent, Star, Crown, Hyacinth, Tulip and Carnation motifs. Nowadays, Turkish designers have begun to use these traditional Turkish motifs in their designs so as to create differences and awareness in the world design. The examples of these industrial designs, using the Turkish motifs, have survived and have Ottoman heritage and historical value. In this study, the Turkish motifs will be examined along with their focus on contemporary Turkish industrial designs used today.

  19. AISMOTIF-An Artificial Immune System for DNA Motif Discovery

    CERN Document Server

    Seeja, K R

    2011-01-01

    Discovery of transcription factor binding sites is a much explored and still exploring area of research in functional genomics. Many computational tools have been developed for finding motifs and each of them has their own advantages as well as disadvantages. Most of these algorithms need prior knowledge about the data to construct background models. However there is not a single technique that can be considered as best for finding regulatory motifs. This paper proposes an artificial immune system based algorithm for finding the transcription factor binding sites or motifs and two new weighted scores for motif evaluation. The algorithm is enumerative, but sufficient pruning of the pattern search space has been incorporated using immune system concepts. The performance of AISMOTIF has been evaluated by comparing it with eight state of art composite motif discovery algorithms and found that AISMOTIF predicts known motifs as well as new motifs from the benchmark dataset without any prior knowledge about the data...

  20. Chaotic motif sampler: detecting motifs from biological sequences by using chaotic neurodynamics

    Science.gov (United States)

    Matsuura, Takafumi; Ikeguchi, Tohru

    Identification of a region in biological sequences, motif extraction problem (MEP) is solved in bioinformatics. However, the MEP is an NP-hard problem. Therefore, it is almost impossible to obtain an optimal solution within a reasonable time frame. To find near optimal solutions for NP-hard combinatorial optimization problems such as traveling salesman problems, quadratic assignment problems, and vehicle routing problems, chaotic search, which is one of the deterministic approaches, has been proposed and exhibits better performance than stochastic approaches. In this paper, we propose a new alignment method that employs chaotic dynamics to solve the MEPs. It is called the Chaotic Motif Sampler. We show that the performance of the Chaotic Motif Sampler is considerably better than that of the conventional methods such as the Gibbs Site Sampler and the Neighborhood Optimization for Multiple Alignment Discovery.

  1. Indole-3-carbinol and 3’, 3’-diindolylmethane modulate androgen effect up-regulation on C-C chemokine ligand 2 and monocyte attraction to prostate cancer cells

    Science.gov (United States)

    Inflammation has a role in prostate tumorigenesis. Recruitment of inflammatory monocytes to the tumor site is mediated by C-C chemokine ligand 2 (CCL2) through binding to its receptor CCR2. We hypothesized that androgen could modulate CCL2 expression in hormone-responsive prostate cancer cells, and ...

  2. Assessing the Exceptionality of Coloured Motifs in Networks

    Directory of Open Access Journals (Sweden)

    Lacroix Vincent

    2009-01-01

    Full Text Available Various methods have been recently employed to characterise the structure of biological networks. In particular, the concept of network motif and the related one of coloured motif have proven useful to model the notion of a functional/evolutionary building block. However, algorithms that enumerate all the motifs of a network may produce a very large output, and methods to decide which motifs should be selected for downstream analysis are needed. A widely used method is to assess if the motif is exceptional, that is, over- or under-represented with respect to a null hypothesis. Much effort has been put in the last thirty years to derive -values for the frequencies of topological motifs, that is, fixed subgraphs. They rely either on (compound Poisson and Gaussian approximations for the motif count distribution in Erdös-Rényi random graphs or on simulations in other models. We focus on a different definition of graph motifs that corresponds to coloured motifs. A coloured motif is a connected subgraph with fixed vertex colours but unspecified topology. Our work is the first analytical attempt to assess the exceptionality of coloured motifs in networks without any simulation. We first establish analytical formulae for the mean and the variance of the count of a coloured motif in an Erdös-Rényi random graph model. Using simulations under this model, we further show that a Pólya-Aeppli distribution better approximates the distribution of the motif count compared to Gaussian or Poisson distributions. The Pólya-Aeppli distribution, and more generally the compound Poisson distributions, are indeed well designed to model counts of clumping events. Altogether, these results enable to derive a -value for a coloured motif, without spending time on simulations.

  3. Bases of motifs for generating repeated patterns with wild cards.

    Science.gov (United States)

    Pisanti, Nadia; Crochemore, Maxime; Grossi, Roberto; Sagot, Marie-France

    2005-01-01

    Motif inference represents one of the most important areas of research in computational biology, and one of its oldest ones. Despite this, the problem remains very much open in the sense that no existing definition is fully satisfying, either in formal terms, or in relation to the biological questions that involve finding such motifs. Two main types of motifs have been considered in the literature: matrices (of letter frequency per position in the motif) and patterns. There is no conclusive evidence in favor of either, and recent work has attempted to integrate the two types into a single model. In this paper, we address the formal issue in relation to motifs as patterns. This is essential to get at a better understanding of motifs in general. In particular, we consider a promising idea that was recently proposed, which attempted to avoid the combinatorial explosion in the number of motifs by means of a generator set for the motifs. Instead of exhibiting a complete list of motifs satisfying some input constraints, what is produced is a basis of such motifs from which all the other ones can be generated. We study the computational cost of determining such a basis of repeated motifs with wild cards in a sequence. We give new upper and lower bounds on such a cost, introducing a notion of basis that is provably contained in (and, thus, smaller) than previously defined ones. Our basis can be computed in less time and space, and is still able to generate the same set of motifs. We also prove that the number of motifs in all bases defined so far grows exponentially with the quorum, that is, with the minimal number of times a motif must appear in a sequence, something unnoticed in previous work. We show that there is no hope to efficiently compute such bases unless the quorum is fixed.

  4. Characteristics of an optimized active metal cast joint between copper and C/C

    Energy Technology Data Exchange (ETDEWEB)

    Schedler, B [Technology Centre of PLANSEE SE, A-6600 Reutte (Austria); Huber, T [Technology Centre of PLANSEE SE, A-6600 Reutte (Austria); Friedrich, T [Technology Centre of PLANSEE SE, A-6600 Reutte (Austria); Eidenberger, E [Department of Physical Metallurgy and Materials Testing, Montanuniversitaet Leoben, A-8700 Leoben (Austria); Kapp, M [Austrian Academy of Sciences, Erich-Schmid-Institute of Material Science, A-8700 Leoben (Austria); Scheu, C [Department of Physical Metallurgy and Materials Testing, Montanuniversitaet Leoben, A-8700 Leoben (Austria); Pippan, R [Austrian Academy of Sciences, Erich-Schmid-Institute of Material Science, A-8700 Leoben (Austria); Clemens, H [Department of Physical Metallurgy and Materials Testing, Montanuniversitaet Leoben, A-8700 Leoben (Austria)

    2007-03-15

    In this paper, an optimized active metal cast copper to carbon composite (C/C) joint is examined. Mechanical characterization by means of shear and tensile tests as well as fracture toughness measurements at ambient temperature are employed, which show that the obtained values are above those of the reference joint that has been used so far. The phases occurring at the interface region and the fracture surface of the optimized joint are investigated in detail to explain the improved mechanical behaviour. The composition and the morphology at the interface region are analysed by means of scanning electron microscopy. In addition, the crack path is analysed by stereomicroscopy. The improved properties can be explained by the circumstance that the fracture of the optimized joint is not restricted to the interface between the occurring carbide and the C/C but changes between C/C, the carbide to C/C interface and the copper, depending on the local structure in the C/C composite.

  5. The MHC motif viewer: a visualization tool for MHC binding motifs

    DEFF Research Database (Denmark)

    Rapin, Nicolas; Hoof, Ilka; Lund, Ole

    2010-01-01

    of peptides, and knowledge of their binding specificities is important for understanding differences in the immune response between individuals. Algorithms predicting which peptides bind a given MHC molecule have recently been developed with high prediction accuracy. The utility of these algorithms...... is hampered by the lack of tools for browsing and comparing specificity of these molecules. We have developed a Web server, MHC Motif Viewer, which allows the display of the binding motif for MHC class I proteins for human, chimpanzee, rhesus monkey, mouse, and swine, as well as HLA-DR protein sequences...

  6. MINER: software for phylogenetic motif identification.

    Science.gov (United States)

    La, David; Livesay, Dennis R

    2005-07-01

    MINER is web-based software for phylogenetic motif (PM) identification. PMs are sequence regions (fragments) that conserve the overall familial phylogeny. PMs have been shown to correspond to a wide variety of catalytic regions, substrate-binding sites and protein interfaces, making them ideal functional site predictions. The MINER output provides an intuitive interface for interactive PM sequence analysis and structural visualization. The web implementation of MINER is freely available at http://www.pmap.csupomona.edu/MINER/. Source code is available to the academic community on request.

  7. DNA motif elucidation using belief propagation

    OpenAIRE

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-01-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the ...

  8. Identification of sequence motifs involved in Dengue virus-host interactions.

    Science.gov (United States)

    Asnet Mary, J; Paramasivan, R; Shenbagarathai, R

    2016-01-01

    Dengue fever is a rapidly spreading mosquito-borne virus infection, which remains a serious global public health problem. As there is no specific treatment or commercial vaccine available for effective control of the disease, the attempts on developing novel control strategies are underway. Viruses utilize the surface receptor proteins of host to enter into the cells. Though various proteins were said to be receptors of Dengue virus (DENV) using Virus Overlay Protein Binding Assay, the precise interaction between DENV and host is not explored. Understanding the structural features of domain III envelope glycoprotein would help in developing efficient antiviral inhibitors. Therefore, an attempt was made to identify the sequence motifs present in domain III envelope glycoprotein of Dengue virus. Computational analysis revealed that the NGR motif is present in the domain III envelope glycoprotein of DENV-1 and DENV-3. Similarly, DENV-1, DENV-2 and DENV-4 were found to contain Yxxphi motif which is a tyrosine-based sorting signal responsible for the interaction with a mu subunit of adaptor protein complex. High-throughput virtual screening resulted in five compounds as lead molecules based on glide score, which ranges from -4.664 to -6.52 kcal/Mol. This computational prediction provides an additional tool for understanding the virus-host interactions and helps to identify potential targets in the host. Further, experimental evidence is warranted to confirm the virus-host interactions and also inhibitory activity of reported lead compounds.

  9. Characterization of Brazed Joints of C-C Composite to Cu-clad-Molybdenum

    Science.gov (United States)

    Singh, M.; Asthana, R.

    2008-01-01

    Carbon-carbon composites with either pitch+CVI matrix or resin-derived matrix were joined to copper-clad molybdenum using two active braze alloys, Cusil-ABA (1.75% Ti) and Ticusil (4.5% Ti). The brazed joints revealed good interfacial bonding, preferential precipitation of Ti at the composite/braze interface, and a tendency toward de-lamination in resin-derived C-C composite due to its low inter-laminar shear strength. Extensive braze penetration of the inter-fiber channels in the pitch+CVI C-C composites was observed. The relatively low brazing temperatures (Cu-clad-Mo/braze interface and higher hardness in Ticusil (approx.85-250 HK) than in Cusil-ABA (approx.50-150 HK). These C-C/Cu-clad-Mo joints with relatively low thermal resistance may be promising for thermal management applications.

  10. RMOD: a tool for regulatory motif detection in signaling network.

    Directory of Open Access Journals (Sweden)

    Jinki Kim

    Full Text Available Regulatory motifs are patterns of activation and inhibition that appear repeatedly in various signaling networks and that show specific regulatory properties. However, the network structures of regulatory motifs are highly diverse and complex, rendering their identification difficult. Here, we present a RMOD, a web-based system for the identification of regulatory motifs and their properties in signaling networks. RMOD finds various network structures of regulatory motifs by compressing the signaling network and detecting the compressed forms of regulatory motifs. To apply it into a large-scale signaling network, it adopts a new subgraph search algorithm using a novel data structure called path-tree, which is a tree structure composed of isomorphic graphs of query regulatory motifs. This algorithm was evaluated using various sizes of signaling networks generated from the integration of various human signaling pathways and it showed that the speed and scalability of this algorithm outperforms those of other algorithms. RMOD includes interactive analysis and auxiliary tools that make it possible to manipulate the whole processes from building signaling network and query regulatory motifs to analyzing regulatory motifs with graphical illustration and summarized descriptions. As a result, RMOD provides an integrated view of the regulatory motifs and mechanism underlying their regulatory motif activities within the signaling network. RMOD is freely accessible online at the following URL: http://pks.kaist.ac.kr/rmod.

  11. Protein functional-group 3D motif and its applications

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Representing and recognizing protein active sites sequence motif (1D motif) and structural motif (3D motif) is an important topic for predicting and designing protein function. Prevalent methods for extracting and searching 3D motif always consider residue as the minimal unit, which have limited sensitivity. Here we present a new spatial representation of protein active sites, called "functional-group 3D motif ", based on the fact that the functional groups inside a residue contribute mostly to its function. Relevant algorithm and computer program are developed, which could be widely used in the function prediction and the study of structural-function relationship of proteins. As a test, we defined a functional-group 3D motif of the catalytic triad and oxyanion hole with the structure of porcine trypsin (PDB code: 1mct) as the template. With our motif-searching program, we successfully found similar sub-structures in trypsins, subtilisins and a/b hydrolases, which show distinct folds but share similar catalytic mechanism. Moreover, this motif can be used to elucidate the structural basis of other proteins with variant catalytic triads by comparing it to those proteins. Finally, we scanned this motif against a non-redundant protein structure database to find its matches, and the results demonstrated the potential application of functional group 3D motif in function prediction. Above all, compared with the other 3D-motif representations on residues, the functional group 3D motif achieves better representation of protein active region, which is more sensitive for protein function prediction.

  12. Monitoring and Diagnostics for C/C++ Real-Time Applications

    CERN Document Server

    Fischer, Yves

    Knowledge about the internal state of computational processes is essential for problem diagnostics as well as for constant monitoring and pre-failure recognition. The CMX li- brary provides monitoring capabilities similiar to the Java Management Extensions (JMX) for C and C++ applications. This thesis provides a detailed analysis of the requirements for monitoring and diagnos- tics of the C/C++ processes at CERN. The developed CMX library enables real-time C/C++ processes to expose values with- out harming their normal execution. CMX is portable and can be integrated in different monitoring architectures.

  13. Experimental study on thermophysical properties of C/C composites at high temperature

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wei; YI Fa-jun; HAN Jie-cai; MENG Song-he

    2006-01-01

    The coefficient of thermal expansion, thermal diffusivity and specific heat of C/C composites from room temperature to ultra high temperature were experimentally investigated. Thermal conductivity and thermal stress resistance of the composites were therefore computed based on experimental results. The results show that the composite has a very low thermal expansion coefficient. Thermal diffusivity decreases exponentially with temperature increase. The specific heat increases linearly as the temperature rises, and the variation trend of thermal conductivity is similar to that of thermal diffusivity. The thermal stress coefficient of C/C composite has little change with temperature variation, and thermal stress resistance of the composite at high temperature is stable.

  14. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    Science.gov (United States)

    Oliveira, Graziele Pereira; Andrade, Ana Cláudia dos Santos Pereira; Rodrigues, Rodrigo Araújo Lima; Arantes, Thalita Souza; Boratto, Paulo Victor Miranda; Silva, Ludmila Karen dos Santos; Dornas, Fábio Pio; Trindade, Giliane de Souza; Drumond, Betânia Paiva; La Scola, Bernard; Kroon, Erna Geessien; Abrahão, Jônatas Santos

    2017-01-01

    For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’) that could be evolved gradually by nucleotides’ gain and loss and point mutations. PMID:28117683

  15. The network motif architecture of dominance hierarchies.

    Science.gov (United States)

    Shizuka, Daizaburo; McDonald, David B

    2015-04-01

    The widespread existence of dominance hierarchies has been a central puzzle in social evolution, yet we lack a framework for synthesizing the vast empirical data on hierarchy structure in animal groups. We applied network motif analysis to compare the structures of dominance networks from data published over the past 80 years. Overall patterns of dominance relations, including some aspects of non-interactions, were strikingly similar across disparate group types. For example, nearly all groups exhibited high frequencies of transitive triads, whereas cycles were very rare. Moreover, pass-along triads were rare, and double-dominant triads were common in most groups. These patterns did not vary in any systematic way across taxa, study settings (captive or wild) or group size. Two factors significantly affected network motif structure: the proportion of dyads that were observed to interact and the interaction rates of the top-ranked individuals. Thus, study design (i.e. how many interactions were observed) and the behaviour of key individuals in the group could explain much of the variations we see in social hierarchies across animals. Our findings confirm the ubiquity of dominance hierarchies across all animal systems, and demonstrate that network analysis provides new avenues for comparative analyses of social hierarchies.

  16. Thymoproteasomes produce unique peptide motifs for positive selection of CD8(+) T cells.

    Science.gov (United States)

    Sasaki, Katsuhiro; Takada, Kensuke; Ohte, Yuki; Kondo, Hiroyuki; Sorimachi, Hiroyuki; Tanaka, Keiji; Takahama, Yousuke; Murata, Shigeo

    2015-01-01

    Positive selection in the thymus provides low-affinity T-cell receptor (TCR) engagement to support the development of potentially useful self-major histocompatibility complex class I (MHC-I)-restricted T cells. Optimal positive selection of CD8(+) T cells requires cortical thymic epithelial cells that express β5t-containing thymoproteasomes (tCPs). However, how tCPs govern positive selection is unclear. Here we show that the tCPs produce unique cleavage motifs in digested peptides and in MHC-I-associated peptides. Interestingly, MHC-I-associated peptides carrying these tCP-dependent motifs are enriched with low-affinity TCR ligands that efficiently induce the positive selection of functionally competent CD8(+) T cells in antigen-specific TCR-transgenic models. These results suggest that tCPs contribute to the positive selection of CD8(+) T cells by preferentially producing low-affinity TCR ligand peptides.

  17. Development of C/C composite for the core component of the high temperature gas cooled reactor

    Energy Technology Data Exchange (ETDEWEB)

    Park, J. Y.; Kim, W. J.; Ryu, W. S.; Jang, J. H

    2005-01-15

    This report reviewed a state of the art on development of C/C composite for the core components for VHTR and described the followings items. The fabrication methods of C/C composites. Summary on the JAERI report (JAERI-Res 2002-026) on the process screening test for the selection of a proper C/C composite material. Review of the proceedings presented at the GEN-IV VHTR material PMB meeting. A status of the domestic commercial C/C composite. The published property data and the characteristics of the commercial C/C composite.

  18. An Affinity Propagation-Based DNA Motif Discovery Algorithm

    Directory of Open Access Journals (Sweden)

    Chunxiao Sun

    2015-01-01

    Full Text Available The planted (l,d motif search (PMS is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.

  19. Triadic motifs in the dependence networks of virtual societies

    CERN Document Server

    Xie, Wen-Jie; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-01-01

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (${\\rm{M}}_9$) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks...

  20. An Affinity Propagation-Based DNA Motif Discovery Algorithm.

    Science.gov (United States)

    Sun, Chunxiao; Huo, Hongwei; Yu, Qiang; Guo, Haitao; Sun, Zhigang

    2015-01-01

    The planted (l, d) motif search (PMS) is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs) in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP) clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM) refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.

  1. Probabilistic models for semisupervised discriminative motif discovery in DNA sequences.

    Science.gov (United States)

    Kim, Jong Kyoung; Choi, Seungjin

    2011-01-01

    Methods for discriminative motif discovery in DNA sequences identify transcription factor binding sites (TFBSs), searching only for patterns that differentiate two sets (positive and negative sets) of sequences. On one hand, discriminative methods increase the sensitivity and specificity of motif discovery, compared to generative models. On the other hand, generative models can easily exploit unlabeled sequences to better detect functional motifs when labeled training samples are limited. In this paper, we develop a hybrid generative/discriminative model which enables us to make use of unlabeled sequences in the framework of discriminative motif discovery, leading to semisupervised discriminative motif discovery. Numerical experiments on yeast ChIP-chip data for discovering DNA motifs demonstrate that the best performance is obtained between the purely-generative and the purely-discriminative and the semisupervised learning improves the performance when labeled sequences are limited.

  2. Dystroglycan versatility in cell adhesion: a tale of multiple motifs

    Directory of Open Access Journals (Sweden)

    Winder Steve J

    2010-02-01

    Full Text Available Abstract Dystroglycan is a ubiquitously expressed heterodimeric adhesion receptor. The extracellular α-subunit makes connections with a number of laminin G domain ligands including laminins, agrin and perlecan in the extracellular matrix and the transmembrane β-subunit makes connections to the actin filament network via cytoskeletal linkers including dystrophin, utrophin, ezrin and plectin, depending on context. Originally discovered as part of the dystrophin glycoprotein complex of skeletal muscle, dystroglycan is an important adhesion molecule and signalling scaffold in a multitude of cell types and tissues and is involved in several diseases. Dystroglycan has emerged as a multifunctional adhesion platform with many interacting partners associating with its short unstructured cytoplasmic domain. Two particular hotspots are the cytoplasmic juxtamembrane region and at the very carboxy terminus of dystroglycan. Regions which between them have several overlapping functions: in the juxtamembrane region; a nuclear localisation signal, ezrin/radixin/moesin protein, rapsyn and ERK MAP Kinase binding function, and at the C terminus a regulatory tyrosine governing WW, SH2 and SH3 domain interactions. We will discuss the binding partners for these motifs and how their interactions and regulation can modulate the involvement of dystroglycan in a range of different adhesion structures and functions depending on context. Thus dystroglycan presents as a multifunctional scaffold involved in adhesion and adhesion-mediated signalling with its functions under exquisite spatio-temporal regulation.

  3. VAMP subfamilies identified by specific R-SNARE motifs.

    Science.gov (United States)

    Rossi, Valeria; Picco, Raffaella; Vacca, Marcella; D'Esposito, Maurizio; D'Urso, Michele; Galli, Thierry; Filippini, Francesco

    2004-05-01

    In eukaryotes, interactions among the alpha-helical coiled-coil domains (CCDs) of soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) play a pivotal role in mediating the fusion among vesicles and target membranes. Surface residues of such CCDs are major candidates to regulate the specificity of membrane fusion, as they may alter local charge at the interaction layers and surface of the fusion complex, possibly modulating its formation and/or the binding of non-SNARE regulatory factors. Based on alternate patterns in surface residues, we have identified two motifs which group vesicular SNAREs in two novel subfamilies: RG-SNAREs and RD-SNAREs. The RG-SNARE CCD is common to all members of the widely conserved family of long VAMPs or longins and to yeast and non-neuronal VAMPs, possibly mediating "basic" fusion mechanisms; instead, only synaptobrevins from Bilateria share an RD-SNARE CCD, which is likely to mediate interactions to specific, yet unknown, regulatory factors and/or be the landmark of rapid fusion reactions like that mediating the release of neurotransmitters.

  4. Preparation of Biomorphic SiC/C Ceramics from Pine Wood via Supercritical Ethanol Infiltration

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Biomorphic (wood derived) carbide ceramics with an overall composition in the SiC/C was produced by supercritical ethanol infiltration of low viscosity tetraethylorthosilicate/supercritical ethanol into biologically derived carbon templates (CB-templates) and in situ hydrolysis into Si(OH)4-gel, the Si(OH)4-gel was calcined at 1400℃ to promote the polycondensation of Si(OH)4-gel into SiO2-phase and then carbonthermal reduction of the SiO2 with the biocarbon template into highly porous, biomorphic SiC/C ceramics. The phases and morphology conversion mechanism of resulting porous SiC/C ceramics have been investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Fourier transform infrared spectroscopy (FT-IR). Experimental results showed that the biomorphic cellular morphology of pinewood charcoal was remained in the porous SiC/C ceramic with high precision that consisted of β-SiC with minority of α-SiC and the remain free carbon existed in amorphous phase.

  5. Revis\\~ao da Constru\\c{c}\\~ao de Modelos Supersim\\'etricos

    CERN Document Server

    Rodríguez, M C

    2001-01-01

    Foi com base neste estudo que fizemos a constru\\c{c}\\~ao da vers\\~ao supersim\\'etrica dos modelos de simetria $SU(3)_{C} \\otimes SU(3)_{L} \\otimes U(1)_{N}$ \\cite{susy331}, apresentado no final da minha tese de doutorado \\cite{mcr1}. Bem como dos estudos fenomenol\\'ogicos subsequente \\cite{mcr}.

  6. Extraction and Visualization of Call Dependencies for Large C/C++ Code Bases : A Comparative Study

    NARCIS (Netherlands)

    Telea, Alexandru; Hoogendorp, Hessel; Ersoy, Ozan; Reniers, Dennie; Lanza, M; Storey, M; Muller, H

    2009-01-01

    Investigating program dependencies such as function calls is challenging for very large systems. We present here an integrated pipeline for extraction and visualization of call-and-hierarchy graphs for C/C++ programs. We present several adaptions and enhancements of a recent visualization method for

  7. Tribological characteristics of C/C-SiC braking composites under dry and wet conditions

    Institute of Scientific and Technical Information of China (English)

    LI Zhuan; XIAO Peng; XIONG Xiang; ZHU Su-hua

    2008-01-01

    C/C-SiC braking composites, based on reinforcement of carbon fibers and rnatrices of carbon and silicon carbide, were fabricated by warm compaction and in situ reaction process. The tribological characteristics of C/C-SiC braking composites under dry and wet conditions were investigated by means of MM-1000 type of friction testing machine. The influence of dry and wet conditions on the tribological characteristics of the C/C-SiC composites was ascertained. Under dry condition, C/C-SiC braking composites show superior tribological characteristics, including high coefficient of friction (0.38), good abrasive resistance (thickness loss is 1.10 μm per cycle) and steady breaking. The main wear mechanism is plastic deformation and abrasion caused by plough. Under wet condition, frictional films form on the worn surface. The coefficient of friction (0.35) could maintain mostly, and the thickness loss (0.70 μm per cycle) reduces to a certain extent. Furthermore, braking curves are steady and adhesion and oxidation are the main wear mechanisms.

  8. Al2O3-SiC-C Bricks for Hot Metal Pretreatment

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ 1 Scope This standard specifies the classification,techni-cal requirements,test methods,inspection rules,packing,marking,transportation,storage and quality certificate of Al2O3-SiC-C bricks for hot metal pre-treatment.

  9. Al2O3 SiC-C Bricks for Hot Metal Pretreatment

    Institute of Scientific and Technical Information of China (English)

    Yu Lingyan; Peng Xigao

    2010-01-01

    @@ 1 Scope This standard specifies the classification,shape and dimensions,technical requirements,test methods,quality appraisal procedures,packing,marking,transportation,storage,and quality certificate of Al2O3SiC-C bricks for hot metal pretreatment.

  10. Re-mediated C-C coupling of pyridines and imidazoles.

    Science.gov (United States)

    Espinal Viguri, Maialen; Huertos, Miguel A; Pérez, Julio; Riera, Lucía; Ara, Irene

    2012-12-19

    Rhenium tricarbonyl complexes with three N-heterocyclic ligands (N-alkylimidazoles or pyridines) undergo deprotonation with KN(SiMe(3))(2) and then oxidation with AgOTf to afford complexes with pyridylimidazole or bipyridine bidentate ligands resulting from deprotonation, C-C coupling and rearomatization.

  11. Imidazole-nitrile or imidazole-isonitrile C-C coupling on rhenium tricarbonyl complexes.

    Science.gov (United States)

    Viguri, Maialen Espinal; Huertos, Miguel A; Pérez, Julio; Riera, Lucía

    2013-09-23

    Ligand activation: Deprotonation of the nitrile or isonitrile complexes [Re(CO)3(N-RIm)2(L)](+) (N-RIm = N-alkylimidazole; L = N≡CtBu, C≡NtBu) selectively afforded alkylidenamido or iminoacyl derivatives, respectively, in which C-C coupling has occurred. Protonation of the latter complex leads to aminocarbene products.

  12. 77 FR 10004 - C$ cMoney, Inc.; Order of Suspension of Trading

    Science.gov (United States)

    2012-02-21

    ... COMMISSION C$ cMoney, Inc.; Order of Suspension of Trading February 16, 2012. It appears to the Securities... the opinion that the public interest and the protection of investors require a suspension of trading... the Securities Exchange Act of 1934, that trading in the securities of the above-listed company...

  13. Detecting DNA regulatory motifs by incorporating positional trendsin information content

    Energy Technology Data Exchange (ETDEWEB)

    Kechris, Katherina J.; van Zwet, Erik; Bickel, Peter J.; Eisen,Michael B.

    2004-05-04

    On the basis of the observation that conserved positions in transcription factor binding sites are often clustered together, we propose a simple extension to the model-based motif discovery methods. We assign position-specific prior distributions to the frequency parameters of the model, penalizing deviations from a specified conservation profile. Examples with both simulated and real data show that this extension helps discover motifs as the data become noisier or when there is a competing false motif.

  14. Photoswitchable triple hydrogen-bonding motif.

    Science.gov (United States)

    Herder, Martin; Pätzel, Michael; Grubert, Lutz; Hecht, Stefan

    2011-01-07

    Photochromic bis(thiazol-4-yl)maleimides, displaying enhanced binding affinity to complementary melamine receptors in their ring-closed switching state, have been developed and could pave the way to light-responsive supramolecular assemblies.

  15. STEME: a robust, accurate motif finder for large data sets.

    Directory of Open Access Journals (Sweden)

    John E Reid

    Full Text Available Motif finding is a difficult problem that has been studied for over 20 years. Some older popular motif finders are not suitable for analysis of the large data sets generated by next-generation sequencing. We recently published an efficient approximation (STEME to the EM algorithm that is at the core of many motif finders such as MEME. This approximation allows the EM algorithm to be applied to large data sets. In this work we describe several efficient extensions to STEME that are based on the MEME algorithm. Together with the original STEME EM approximation, these extensions make STEME a fully-fledged motif finder with similar properties to MEME. We discuss the difficulty of objectively comparing motif finders. We show that STEME performs comparably to existing prominent discriminative motif finders, DREME and Trawler, on 13 sets of transcription factor binding data in mouse ES cells. We demonstrate the ability of STEME to find long degenerate motifs which these discriminative motif finders do not find. As part of our method, we extend an earlier method due to Nagarajan et al. for the efficient calculation of motif E-values. STEME's source code is available under an open source license and STEME is available via a web interface.

  16. Complex lasso: new entangled motifs in proteins

    Science.gov (United States)

    Niemyska, Wanda; Dabrowski-Tumanski, Pawel; Kadlof, Michal; Haglund, Ellinor; Sułkowski, Piotr; Sulkowska, Joanna I.

    2016-11-01

    We identify new entangled motifs in proteins that we call complex lassos. Lassos arise in proteins with disulfide bridges (or in proteins with amide linkages), when termini of a protein backbone pierce through an auxiliary surface of minimal area, spanned on a covalent loop. We find that as much as 18% of all proteins with disulfide bridges in a non-redundant subset of PDB form complex lassos, and classify them into six distinct geometric classes, one of which resembles supercoiling known from DNA. Based on biological classification of proteins we find that lassos are much more common in viruses, plants and fungi than in other kingdoms of life. We also discuss how changes in the oxidation/reduction potential may affect the function of proteins with lassos. Lassos and associated surfaces of minimal area provide new, interesting and possessing many potential applications geometric characteristics not only of proteins, but also of other biomolecules.

  17. Modeling Network Evolution Using Graph Motifs

    CERN Document Server

    Conway, Drew

    2011-01-01

    Network structures are extremely important to the study of political science. Much of the data in its subfields are naturally represented as networks. This includes trade, diplomatic and conflict relationships. The social structure of several organization is also of interest to many researchers, such as the affiliations of legislators or the relationships among terrorist. A key aspect of studying social networks is understanding the evolutionary dynamics and the mechanism by which these structures grow and change over time. While current methods are well suited to describe static features of networks, they are less capable of specifying models of change and simulating network evolution. In the following paper I present a new method for modeling network growth and evolution. This method relies on graph motifs to generate simulated network data with particular structural characteristic. This technique departs notably from current methods both in form and function. Rather than a closed-form model, or stochastic ...

  18. Motif-role-fingerprints: the building-blocks of motifs, clustering-coefficients and transitivities in directed networks.

    Directory of Open Access Journals (Sweden)

    Mark D McDonnell

    Full Text Available Complex networks are frequently characterized by metrics for which particular subgraphs are counted. One statistic from this category, which we refer to as motif-role fingerprints, differs from global subgraph counts in that the number of subgraphs in which each node participates is counted. As with global subgraph counts, it can be important to distinguish between motif-role fingerprints that are 'structural' (induced subgraphs and 'functional' (partial subgraphs. Here we show mathematically that a vector of all functional motif-role fingerprints can readily be obtained from an arbitrary directed adjacency matrix, and then converted to structural motif-role fingerprints by multiplying that vector by a specific invertible conversion matrix. This result demonstrates that a unique structural motif-role fingerprint exists for any given functional motif-role fingerprint. We demonstrate a similar result for the cases of functional and structural motif-fingerprints without node roles, and global subgraph counts that form the basis of standard motif analysis. We also explicitly highlight that motif-role fingerprints are elemental to several popular metrics for quantifying the subgraph structure of directed complex networks, including motif distributions, directed clustering coefficient, and transitivity. The relationships between each of these metrics and motif-role fingerprints also suggest new subtypes of directed clustering coefficients and transitivities. Our results have potential utility in analyzing directed synaptic networks constructed from neuronal connectome data, such as in terms of centrality. Other potential applications include anomaly detection in networks, identification of similar networks and identification of similar nodes within networks. Matlab code for calculating all stated metrics following calculation of functional motif-role fingerprints is provided as S1 Matlab File.

  19. Encoded expansion: an efficient algorithm to discover identical string motifs.

    Directory of Open Access Journals (Sweden)

    Aqil M Azmi

    Full Text Available A major task in computational biology is the discovery of short recurring string patterns known as motifs. Most of the schemes to discover motifs are either stochastic or combinatorial in nature. Stochastic approaches do not guarantee finding the correct motifs, while the combinatorial schemes tend to have an exponential time complexity with respect to motif length. To alleviate the cost, the combinatorial approach exploits dynamic data structures such as trees or graphs. Recently (Karci (2009 Efficient automatic exact motif discovery algorithms for biological sequences, Expert Systems with Applications 36:7952-7963 devised a deterministic algorithm that finds all the identical copies of string motifs of all sizes [Formula: see text] in theoretical time complexity of [Formula: see text] and a space complexity of [Formula: see text] where [Formula: see text] is the length of the input sequence and [Formula: see text] is the length of the longest possible string motif. In this paper, we present a significant improvement on Karci's original algorithm. The algorithm that we propose reports all identical string motifs of sizes [Formula: see text] that occur at least [Formula: see text] times. Our algorithm starts with string motifs of size 2, and at each iteration it expands the candidate string motifs by one symbol throwing out those that occur less than [Formula: see text] times in the entire input sequence. We use a simple array and data encoding to achieve theoretical worst-case time complexity of [Formula: see text] and a space complexity of [Formula: see text] Encoding of the substrings can speed up the process of comparison between string motifs. Experimental results on random and real biological sequences confirm that our algorithm has indeed a linear time complexity and it is more scalable in terms of sequence length than the existing algorithms.

  20. The limits of de novo DNA motif discovery.

    Directory of Open Access Journals (Sweden)

    David Simcha

    Full Text Available A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery-searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA "background" sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are "too null," resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where "ground truth" is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced "over-fitting" in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of

  1. Leishmania-induced IRAK-1 inactivation is mediated by SHP-1 interacting with an evolutionarily conserved KTIM motif.

    Directory of Open Access Journals (Sweden)

    Issa Abu-Dayyeh

    Full Text Available Parasites of the Leishmania genus can rapidly alter several macrophage (MØ signalling pathways in order to tame down the innate immune response and inflammation, therefore favouring their survival and propagation within their mammalian host. Having recently reported that Leishmania and bacterial LPS generate a significantly stronger inflammatory response in animals and phagocytes functionally deficient for the Src homology 2 domain-containing protein tyrosine phosphatase (SHP-1, we hypothesized that Leishmania could exploit SHP-1 to inactivate key kinases involved in Toll-like receptor (TLR signalling and innate immunity such as IL-1 receptor-associated kinase 1 (IRAK-1. Here we show that upon infection, SHP-1 rapidly binds to IRAK-1, completely inactivating its intrinsic kinase activity and any further LPS-mediated activation as well as MØ functions. We also demonstrate that the SHP-1/IRAK-1 interaction occurs via an evolutionarily conserved ITIM-like motif found in the kinase domain of IRAK-1, which we named KTIM (Kinase Tyrosyl-based Inhibitory Motif. This regulatory motif appeared in early vertebrates and is not found in any other IRAK family member. Our study additionally reveals that several other kinases (e.g. Erk1/2, IKKalpha/beta involved in downstream TLR signalling also bear KTIMs in their kinase domains and interact with SHP-1. We thus provide the first demonstration that a pathogen can exploit a host protein tyrosine phosphatase, namely SHP-1, to directly inactivate IRAK-1 through a generally conserved KTIM motif.

  2. NCBI nr-aa BLAST: CBRC-ETEL-01-1350 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-ETEL-01-1350 ref|NP_001001620.1| CC chemokine receptor 3 [Sus scrofa] dbj|BAD0...8659.1| chemokine (C-C motif) receptor 3 [Sus scrofa] dbj|BAD12132.1| chemokine C-C motif receptor 3 [Sus scrofa...] dbj|BAD12133.1| chemokine C-C motif receptor 3 [Sus scrofa] NP_001001620.1 1e-144 71% ...

  3. NCBI nr-aa BLAST: CBRC-EEUR-01-0018 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-EEUR-01-0018 ref|NP_001001620.1| CC chemokine receptor 3 [Sus scrofa] dbj|BAD0...8659.1| chemokine (C-C motif) receptor 3 [Sus scrofa] dbj|BAD12132.1| chemokine C-C motif receptor 3 [Sus scrofa...] dbj|BAD12133.1| chemokine C-C motif receptor 3 [Sus scrofa] NP_001001620.1 1e-105 75% ...

  4. Mast Cell and Immune Inhibitory Receptors

    Institute of Scientific and Technical Information of China (English)

    LixinLi; ZhengbinYao

    2004-01-01

    Modulation by balancing activating and inhibitory receptors constitutes an important mechanism for regulating immune responses. Cells that are activated following ligation of receptors bearing immunoreceptor tyrosine-based activation motifs (ITAMs) can be negatively regulated by other receptors bearing immunoreceptor tyrosine-based inhibition motifs (ITIMs). Human mast cells (MCs) are the major effector cells of type I hypersensitivity and important participants in a number of disease processes. Antigen-mediated aggregation of IgE bound to its high-affinity receptor on MCs initiates a complex series of biochemical events leading to MC activation. With great detailed description and analysis of several inhibitory receptors on human MCs, a central paradigm of negative regulation of human MC activation by these receptors has emerged. Cellular & Molecular Immunology. 2004;1(6):408-415.

  5. Probing structural changes of self assembled i-motif DNA

    KAUST Repository

    Lee, Iljoon

    2015-01-01

    We report an i-motif structural probing system based on Thioflavin T (ThT) as a fluorescent sensor. This probe can discriminate the structural changes of RET and Rb i-motif sequences according to pH change. This journal is

  6. Discovering large network motifs from a complex biological network

    Energy Technology Data Exchange (ETDEWEB)

    Terada, Aika; Sese, Jun, E-mail: terada@sel.is.ocha.ac.j, E-mail: sesejun@is.ocha.ac.j [Department of Computer Science, Ochanomizu University, 2-1-1 Ohtsuka, Bunkyo-ku, Tokyo 112-8610 (Japan)

    2009-12-01

    Graph structures representing relationships between entries have been studied in statistical analysis, and the results of these studies have been applied to biological networks, whose nodes and edges represent proteins and the relationships between them, respectively. Most of the studies have focused on only graph structures such as scale-free properties and cliques, but the relationships between nodes are also important features since most of the proteins perform their functions by connecting to other proteins. In order to determine such relationships, the problem of network motif discovery has been addressed; network motifs are frequently appearing graph structures in a given graph. However, the methods for network motif discovery are highly restrictive for the application to biological network because they can only be used to find small network motifs or they do not consider noise and uncertainty in observations. In this study, we introduce a new index to measure network motifs called AR index and develop a novel algorithm called ARIANA for finding large motifs even when the network has noise. Experiments using a synthetic network verify that our method can find better network motifs than an existing algorithm. By applying ARIANA to a real complex biological network, we find network motifs associated with regulations of start time of cell functions and generation of cell energies and discover that the cell cycle proteins can be categorized into two different groups.

  7. Motif Participation by Genes in E. coli Transcriptional Networks

    Directory of Open Access Journals (Sweden)

    Michael eMayo

    2012-09-01

    Full Text Available Motifs are patterns of recurring connections among the genes of genetic networks that occur more frequently than would be expected from randomized networks with the same degree sequence. Although the abundance of certain three-node motifs, such as the feed-forward loop, is positively correlated with a networks’ ability to tolerate moderate disruptions to gene expression, little is known regarding the connectivity of individual genes participating in multiple motifs. Using the transcriptional network of the bacterium Escherichia coli, we investigate this feature by reconstructing the distribution of genes participating in feed-forward loop motifs from its largest connected network component. We contrast these motif participation distributions with those obtained from model networks built using the preferential attachment mechanism employed by many biological and man-made networks. We report that, although some of these model networks support a motif participation distribution that appears qualitatively similar to that obtained from the bacterium Escherichia coli, the probability for a node to support a feed-forward loop motif may instead be strongly influenced by only a few master transcriptional regulators within the network. From these analyses we conclude that such master regulators may be a crucial ingredient to describe coupling among feed-forward loop motifs in transcriptional regulatory networks.

  8. Thermo-mechanical and tribological properties of phenolic polymers composites and C-C composites

    Directory of Open Access Journals (Sweden)

    Virgil MARINESCU

    2010-12-01

    Full Text Available Formaldehyde resin-based composites have been an inaugural step in obtaining and usingcomposite materials and they have grown rapidly because of their multiple uses, especially inelectrical and aeronautical field.Phenolic matrix composites represent a preliminary study to obtain mezophase carbon-carboncomposites for advanced materials as potential solutions for reentry shields of cosmic vehicles andlaunch subsystems, as elements of modern braking systems in aircraft or as potential solutions for thecomponents of the combustion chamber of rockets and also as hypersonic transport solutions for thefuture. Both phenolic matrix laminated composites and C-C mezophase matrix C-C composites wereobtained.This paper presents an evaluation of the mechanical and tribological behavior of the obtainedcomposites.

  9. Influence of additives on oxidation resistance of binderless C/C composite

    Institute of Scientific and Technical Information of China (English)

    周声劢; 刘其城; 胡晓凯

    2003-01-01

    Experiment of adding B4C, SiC, and Si powders to improve oxidation resistance of the C/C compositeswas carried out. The results show that the increase of oxidation resistance is remarkable when the contents of B4C,SiC, and Si powders are 10%, 10%, and 5% in the composites, respectively. The regularities and mechanism ofthe effects of the ceramic powders on the oxidation resistance of the composites were also discussed.

  10. Photoinduced C-C Cross-Coupling of Aryl Chlorides and Inert Arenes

    Directory of Open Access Journals (Sweden)

    Lele Wang

    2016-01-01

    Full Text Available Here we report a facile, efficient, and catalyst-free method to realize C-C cross-coupling of aryl chlorides and inert arenes under UV light irradiation. The aryl radical upon homolytic cleavage of C-Cl bond initiated the nucleophilic substitution reaction with inert arenes to give biaryl products. This mild reaction mode can also be applied to other synthetic reactions, such as the construction of C-N bonds and trifluoromethylated compounds.

  11. Long-term tropospheric trend of octafluorocyclobutane (c-C4F8 or PFC-318

    Directory of Open Access Journals (Sweden)

    T. Röckmann

    2012-01-01

    Full Text Available Air samples collected at Cape Grim, Tasmania between 1978 and 2008 and during a series of more recent aircraft sampling programmes have been analysed to determine the atmospheric abundance and trend of octafluorocyclobutane (c-C4F8 or PFC-318. c-C4F8 has an atmospheric lifetime in excess of 3000 yr and a global warming potential (GWP of 10 300 (100 yr time horizon, making it one of the most potent greenhouse gases detected in the atmosphere to date. The abundance of c-C4F8 in the Southern Hemisphere has risen from 0.35 ppt in 1978 to 1.2 ppt in 2010, and is currently increasing at a rate of around 0.03 ppt yr−1. It is the third most abundant perfluorocarbon (PFC in the present day atmosphere, behind CF4 (~75 ppt and C2F6 (~4 ppt. Although a number of potential sources of c-C4F8 have been reported, including the electronics and semi-conductor industries, there remains a large discrepancy in the atmospheric budget. Using a 2-D global model to derive top-down global emissions based on the Cape Grim measurements yields a recent (2007 emission rate of around 1.1 Gg yr−1 and a cumulative emission up to and including 2007 of 38.1 Gg. Emissions reported on the EDGAR emissions database for the period 1986–2005 represent less than 1% of the top-down emissions for the same period, which suggests there is a large unaccounted for source of this compound. It is also apparent that the magnitude of this source has varied considerably over the past 30 yr, declining sharply in the late 1980s before increasing again in the mid-1990s.

  12. Dynamic Motifs of Strategies in Prisoner's Dilemma Games

    CERN Document Server

    Kim, Young Jin; Jeong, Seon-Young; Son, Seung-Woo

    2014-01-01

    We investigate the win-lose relations between strategies of iterated prisoner's dilemma games by using a directed network concept to display the replicator dynamics results. In the giant strongly-connected component of the win/lose network, we find win-lose circulations similar to rock-paper-scissors and analyze the fixed point and its stability. Applying the network motif concept, we introduce dynamic motifs, which describe the population dynamics relations among the three strategies. Through exact enumeration, we find 22 dynamic motifs and display their phase portraits. Visualization using directed networks and motif analysis is a useful method to make complex dynamic behavior simple in order to understand it more intuitively. Dynamic motifs can be building blocks for dynamic behavior among strategies when they are applied to other types of games.

  13. Dynamic motifs of strategies in prisoner's dilemma games

    Science.gov (United States)

    Kim, Young Jin; Roh, Myungkyoon; Jeong, Seon-Young; Son, Seung-Woo

    2014-12-01

    We investigate the win-lose relations between strategies of iterated prisoner's dilemma games by using a directed network concept to display the replicator dynamics results. In the giant strongly-connected component of the win/lose network, we find win-lose circulations similar to rock-paper-scissors and analyze the fixed point and its stability. Applying the network motif concept, we introduce dynamic motifs, which describe the population dynamics relations among the three strategies. Through exact enumeration, we find 22 dynamic motifs and display their phase portraits. Visualization using directed networks and motif analysis is a useful method to make complex dynamic behavior simple in order to understand it more intuitively. Dynamic motifs can be building blocks for dynamic behavior among strategies when they are applied to other types of games.

  14. BlockLogo: Visualization of peptide and sequence motif conservation

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian

    2013-01-01

    BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment......, selection of motif positions, type of sequence, and output format definition. The output has BlockLogo along with the sequence logo, and a table of motif frequencies. We deployed BlockLogo as an online application and have demonstrated its utility through examples that show visualization of T-cell epitopes...... and B-cell epitopes (both continuous and discontinuous). Our additional example shows a visualization and analysis of structural motifs that determine the specificity of peptide binding to HLA-DR molecules. The BlockLogo server also employs selected experimentally validated prediction algorithms...

  15. An algorithm for motif-based network design

    CERN Document Server

    Mäki-Marttunen, Tuomo

    2016-01-01

    A determinant property of the structure of a biological network is the distribution of local connectivity patterns, i.e., network motifs. In this work, a method for creating directed, unweighted networks while promoting a certain combination of motifs is presented. This motif-based network algorithm starts with an empty graph and randomly connects the nodes by advancing or discouraging the formation of chosen motifs. The in- or out-degree distribution of the generated networks can be explicitly chosen. The algorithm is shown to perform well in producing networks with high occurrences of the targeted motifs, both ones consisting of 3 nodes as well as ones consisting of 4 nodes. Moreover, the algorithm can also be tuned to bring about global network characteristics found in many natural networks, such as small-worldness and modularity.

  16. Monte Carlo Simulation of Electron Swarms Parameters in c-C4F8/CF4 Gas Mixtures

    Institute of Scientific and Technical Information of China (English)

    LIU Xue-li; XIAO Deng-ming; WANG Yan-an; ZHANG Zhou-sheng

    2008-01-01

    The swarm parametes for c-C4F8/CF4 mixtures, including the density-normalized effective ionization coefficient, drift velocity and mean energy were calculated using Monte-Carlo method with the null collision technique. The overall density-reduced electric field strength could be varied between 150 and 500 Td,while the c-C4F8 content in gas mixtures is varied in the range of 0-100%. The value of the density-normalize deffective ionization coefficient shows a strong dependence on the c-C4F8 content, becoming more electronegative as the content of c-C4F8 is increased. The drift velocity of c-C4F4/CF4 mixtures is more affected by CF4. The calculated limiting field strength for c-C4F8/CF4 mixtures is higher than that of SF6/CF4.

  17. Building Bridges: Biocatalytic C-C-Bond Formation toward Multifunctional Products.

    Science.gov (United States)

    Schmidt, Nina G; Eger, Elisabeth; Kroutil, Wolfgang

    2016-07-01

    Carbon-carbon bond formation is the key reaction for organic synthesis to construct the carbon framework of organic molecules. The review gives a selection of biocatalytic C-C-bond-forming reactions which have been investigated during the last 5 years and which have already been proven to be applicable for organic synthesis. In most cases, the reactions lead to products functionalized at the site of C-C-bond formation (e.g., α-hydroxy ketones, aminoalcohols, diols, 1,4-diketones, etc.) or allow to decorate aromatic and heteroaromatic molecules. Furthermore, examples for cyclization of (non)natural precursors leading to saturated carbocycles are given as well as the stereoselective cyclopropanation of olefins affording cyclopropanes. Although many tools are already available, recent research also makes it clear that nature provides an even broader set of enzymes to perform specific C-C coupling reactions. The possibilities are without limit; however, a big library of variants for different types of reactions is required to have the specific enzyme for a desired specific (stereoselective) reaction at hand.

  18. C/C-SiC Composites for Nozzle of Solid Propellant Ramjet

    Directory of Open Access Journals (Sweden)

    WANG Lingling

    2017-01-01

    Full Text Available Carbon fiber reinforced carbon and silicon carbide matrix composites for nozzle inner of solid propellant ramjet were prepared by using the hybrid process of "chemical vapor infiltration + precursor impregnation pyrolysis (CVI+PIP". The microstructure, flexural and anti-ablation properties of the C/C-SiC composites and hydraulic test and rocket motor hot firing test for nozzle inner of solid propellant ramjet were comprehensively investigated. The results show that when the flexural strength of the composite reachs 197 MPa, the fracture damage behavior of the composites presents typical toughness mode.Also the composites has excellent anti-ablative property, i.e., linear ablation rate is only 0.0063 mm·s-1 after 200 s ablation. The C/C-SiC component have excellent integral bearing performance with the hydraulic bursting pressure of 6.5 MPa, and the high temperature combination property of the C/C-SiC composite nozzle inner is verified through motor hot firing of solid propellant ramjet.

  19. Active Brazing of C/C Composite to Copper by AgCuTi Filler Metal

    Science.gov (United States)

    Zhang, Kexiang; Xia, Lihong; Zhang, Fuqin; He, Lianlong

    2016-05-01

    Brazing between the carbon-fiber-reinforced carbon composite (C/C composite) and copper has gained increasing interest because of its important application in thermal management systems in nuclear fusion reactors and in the aerospace industry. In order to examine the "interfacial shape effect" on the mechanical properties of the joint, straight and conical interfacial configurations were designed and machined on the surface of C/C composites before joining to copper using an Ag-68.8Cu-4.5Ti (wt pct) alloy. The microstructure and interfacial microchemistry of C/C composite/AgCuTi/Cu brazed joints were comprehensively investigated by using high-resolution transmission electron microscopy. The results indicate that the joint region of both straight and conical joints can be described as a bilayer. Reaction products of Cu3Ti3O and γ-TiO were formed near the copper side in a conical interface joint, while no reaction products were found in the straight case. The effect of Ag on the interfacial reaction was discussed, and the formation mechanism of the joints during brazing was proposed. On the basis of the detailed microstructure presented, the mechanical performance of the brazed joints was discussed in terms of reaction and morphology across the joint.

  20. A C/C++ Build System Based On Maven for the LHC Controls System

    CERN Document Server

    Nguyen Xuan, J; Dönszelmann, M

    2011-01-01

    The CERN accelerator controls system, mainly written in Java and C/C++, consists nowadays of 50 projects and 150 active developers. The controls group has decided to unify the development process and standards (e.g. project layout) using Apache Maven and Sonatype Nexus. Maven is the de-facto build tool for Java, it deals with versioning and dependency management, whereas Nexus is a repository manager. C/C++ developers were struggling to keep their dependencies on other CERN projects, as no versioning was applied, the libraries have to be compiled and available for several platforms and architectures, and finally there was no dependency management mechanism. This results in very complex Makefiles which were difficult to maintain. Even if Maven is primarily designed for Java, a plugin (Maven NAR) adapts the build process for native programming languages for different operating systems and platforms. However C/C++ developers were not keen to abandon their current Makefiles. Hence our approach was to combine the ...

  1. A new C=C embedded porphyrin sheet with superior oxygen reduction performance

    Institute of Scientific and Technical Information of China (English)

    Yawei Li[1; Shunhong Zhang[2; Jiabing Yu[1; Qian Wang[2; Qiang Sun[1,2,3; Puru Jena[3

    2015-01-01

    C2 is a well-known pseudo-oxygen unit with an electron affinity of 3.4 eV. We show that it can exhibit metal-ion like behavior when embedded in a porphyrin sheet and form a metal-free two-dimensional material with superior oxygen reduction performance. Here, the positively charged C=C units are highly active for oxygen reduction reaction (ORR) via dissociation pathways with a small energy barrier of 0.09 eV, much smaller than that of other non-platinum group metal (non-PGM) ORR catalysts. Using a microkinetics-based model we calculated the partial current density to be 3.0 mA/cm2 at 0.65 V vs. a standard hydrogen electrode (SHE), which is comparable to that of the state-of-the-art Pt/C catalyst. We further confirm that the C=C embedded porphyrin sheet is dynamically and thermally stable with a quasi-direct band gap of 1.14 eV. The superior catalytic performance and geometric stability make the metal-free C=C porphyrin sheet ideal for fuel cell applications.

  2. Determination of material properties for short fibre reinforced C/C-SiC

    Directory of Open Access Journals (Sweden)

    Hausherr J.-M.

    2015-01-01

    Full Text Available Determining the mechanical properties of short fibre reinforced CMC using standard sized coupons has always been a challenge due to a high statistical scattering of the measured values. Although the random orientation of short fibres results in a quasi-isotropic material behavior of 2D-structures with a sufficiently large volume, the small volume typical for test coupons usually results in a non-isotropic fibre orientation in the tested volume. This paper describes a method for manufacturing unidirectional oriented short fibre reinforced CMC materials and presents material properties of UD-C/C-SiC. After verifying the fibre orientation of the CMC using micro-computed tomography, coupons were extracted to determine the orthotropic material properties. These orthotropic material properties were then used to predict the properties of C/C-SiC with randomly distributed short fibres. To validate the method, micro-computed tomography is used to quantitatively determine the fibre orientation within coupons extracted from randomly distributed short fibre C/C-SiC. After mechanical three-point-bending tests, the measured stiffness and bending strength is compared with the predicted properties. Finally, the data are used to devise a method suited for reducing the inherent large spread of material properties associated with the measurement of CMC materials with randomly distributed short fibres.

  3. PH motifs in PAR1&2 endow breast cancer growth

    Science.gov (United States)

    Kancharla, A.; Maoz, M.; Jaber, M.; Agranovich, D.; Peretz, T.; Grisaru-Granovsky, S.; Uziely, B.; Bar-Shavit, R.

    2015-01-01

    Although emerging roles of protease-activated receptor1&2 (PAR1&2) in cancer are recognized, their underlying signalling events are poorly understood. Here we show signal-binding motifs in PAR1&2 that are critical for breast cancer growth. This occurs via the association of the pleckstrin homology (PH) domain with Akt/PKB as a key signalling event of PARs. Other PH-domain signal-proteins such as Etk/Bmx and Vav3 also associate with PAR1 and PAR2 through their PH domains. PAR1 and PAR2 bind with priority to Etk/Bmx. A point mutation in PAR2, H349A, but not in R352A, abrogates PH-protein association and is sufficient to markedly reduce PAR2-instigated breast tumour growth in vivo and placental extravillous trophoblast (EVT) invasion in vitro. Similarly, the PAR1 mutant hPar1-7A, which is unable to bind the PH domain, reduces mammary tumours and EVT invasion, endowing these motifs with physiological significance and underscoring the importance of these previously unknown PAR1 and PAR2 PH-domain-binding motifs in both pathological and physiological invasion processes. PMID:26600192

  4. Automatic annotation of protein motif function with Gene Ontology terms

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Vanathi

    2004-09-01

    Full Text Available Abstract Background Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.

  5. De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes.

    Science.gov (United States)

    Zolotarov, Yevgen; Strömvik, Martina

    2015-01-01

    Plants accumulate dehydrins in response to osmotic stresses. Dehydrins are divided into five different classes, which are thought to be regulated in different manners. To better understand differences in transcriptional regulation of the five dehydrin classes, de novo motif discovery was performed on 350 dehydrin promoter sequences from a total of 51 plant genomes. Overrepresented motifs were identified in the promoters of five dehydrin classes. The Kn dehydrin promoters contain motifs linked with meristem specific expression, as well as motifs linked with cold/dehydration and abscisic acid response. KS dehydrin promoters contain a motif with a GATA core. SKn and YnSKn dehydrin promoters contain motifs that match elements connected with cold/dehydration, abscisic acid and light response. YnKn dehydrin promoters contain motifs that match abscisic acid and light response elements, but not cold/dehydration response elements. Conserved promoter motifs are present in the dehydrin classes and across different plant lineages, indicating that dehydrin gene regulation is likely also conserved.

  6. Exchanging Alkyl Groups through Unstrained C-C Bond Cleavage in the Presence of a Copper Catalyst.

    Science.gov (United States)

    Wada, Masaru; Noda, Yushi; Nishikata, Takashi

    2017-04-05

    Although numerous reports exist on strained C-C bond cleavage reactions in aryl substitutions, the cleavage methodology for unstrained C-C bonds in alkylation reactions has not yet been established. We found that unstrained allylic C-C bonds can be cleaved using α-radicals to form C(sp(3) )-C(sp(3) ) bonds in the presence of a copper catalyst. In this reaction, the property of leaving and loading radicals is very important for radical fragmentations. In this paper, we investigated the effects of these properties in cleavage reactions for unstrained C-C bonds.

  7. Motif-specific sampling of phosphoproteomes.

    Science.gov (United States)

    Ruse, Cristian I; McClatchy, Daniel B; Lu, Bingwen; Cociorva, Daniel; Motoyama, Akira; Park, Sung Kyu; Yates, John R

    2008-05-01

    Phosphoproteomics, the targeted study of a subfraction of the proteome which is modified by phosphorylation, has become an indispensable tool to study cell signaling dynamics. We described a methodology that linked phosphoproteome and proteome analysis based on Ba2+ binding properties of amino acids. This technology selected motif-specific phosphopeptides independent of the system under analysis. MudPIT (Multidimensional Identification Technology) identified 1037 precipitated phosphopeptides from as little as 250 microg of proteins. To extend coverage of the phosphoproteome, we sampled the nuclear extract of HeLa cells with three values of Ba2+ ions molarity. The presence of more than 70% of identified phosphoproteins was further substantiated by their nonmodified peptides. Upon isoproterenol stimulation of HEK cells, we identified an increasing number of phosphoproteins from MAPK cascades and AKAP signaling hubs. We quantified changes in both protein and phosphorylation levels of 197 phosphoproteins including a critical kinase, MAPK1. Integration of differential phosphorylation of MAPK1 with knowledge bases constructed modules that correlated well with its role as node in cross-talk of canonical pathways.

  8. Strategi Mengenali Motif Khas Kain Tenun Cual Bangka Dengan AHP

    Directory of Open Access Journals (Sweden)

    Hilyah Magdalena

    2016-12-01

    Full Text Available Woven fabric cual Bangka currently used as one of the identity of community pride in Bangka Belitung Islands. The specificity of this fart cual fabric interesting to study because of the motives that have similarities with songket palembang. Woven fabric cual Bangka and Palembang songket cloth looks similar because the same cloth-making techniques - both using techniques sungkit. The purpose of this research is how to recognize a particular motif woven fabric cual fart. This research using Analytical Hierarchy Process ( AHP to classify some specific motifs that exist in woven fabric cual fart. Experts in the field of woven fabric cual is to inform you that the woven fabric cual farts have tabled motif, motifs or patterns, motifs fabric edge, motif gold thread, fabric base material, as well as the specific color. The research involved four experts that the results of the questionnaires is processed by software Expert Choice 2000. The results showed that the main peculiarity of the woven fabric cual fart is in a pattern or motif with a percentage of 31.5, and is the chosen alternative product is songket with a percentage of 25.4.

  9. Computational analyses of synergism in small molecular network motifs.

    Directory of Open Access Journals (Sweden)

    Yili Zhang

    2014-03-01

    Full Text Available Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically to alter the responses of the motifs to stimuli. Synergism (or antagonism was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions.

  10. Triadic motifs in the dependence networks of virtual societies

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-01

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  11. Role of N-glycosylation sites and CXC motifs in trafficking of Medicago trunculata Nod Factor Perception protein to the plasma membrane.

    NARCIS (Netherlands)

    Lefebvre, B.; Klaus-Heisen, D.; Pietraszewska-Bogiel, A.; Hervé, M.; Camut, S.; Auriac, M.C.; Gasciolli, V.; Nurisso, A.; Gadella, T.W.; Cullimore, J.

    2012-01-01

    The lysin motif receptor like kinase, NFP, is a key protein in the legume Medicago truncatula for the perception of lipochitooligosaccharidic Nod Factors, which are secreted bacterial signals essential for establishing the nitrogen-fixing legume-rhizobia symbiosis. Predicted structural and genetic a

  12. A speedup technique for (l, d-motif finding algorithms

    Directory of Open Access Journals (Sweden)

    Dinh Hieu

    2011-03-01

    Full Text Available Abstract Background The discovery of patterns in DNA, RNA, and protein sequences has led to the solution of many vital biological problems. For instance, the identification of patterns in nucleic acid sequences has resulted in the determination of open reading frames, identification of promoter elements of genes, identification of intron/exon splicing sites, identification of SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have proven to be extremely helpful in domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, etc. Motifs are important patterns that are helpful in finding transcriptional regulatory elements, transcription factor binding sites, functional genomics, drug design, etc. As a result, numerous papers have been written to solve the motif search problem. Results Three versions of the motif search problem have been proposed in the literature: Simple Motif Search (SMS, (l, d-motif search (or Planted Motif Search (PMS, and Edit-distance-based Motif Search (EMS. In this paper we focus on PMS. Two kinds of algorithms can be found in the literature for solving the PMS problem: exact and approximate. An exact algorithm identifies the motifs always and an approximate algorithm may fail to identify some or all of the motifs. The exact version of PMS problem has been shown to be NP-hard. Exact algorithms proposed in the literature for PMS take time that is exponential in some of the underlying parameters. In this paper we propose a generic technique that can be used to speedup PMS algorithms. Conclusions We present a speedup technique that can be used on any PMS algorithm. We have tested our speedup technique on a number of algorithms. These experimental results show that our speedup technique is indeed very

  13. Of ITIMs, ITAMs, and ITAMis: revisiting immunoglobulin Fc receptor signaling.

    Science.gov (United States)

    Getahun, Andrew; Cambier, John C

    2015-11-01

    Receptors for immunoglobulin Fc regions play multiple critical roles in the immune system, mediating functions as diverse as phagocytosis, triggering degranulation of basophils and mast cells, promoting immunoglobulin class switching, and preventing excessive activation. Transmembrane signaling associated with these functions is mediated primarily by two amino acid sequence motifs, ITAMs (immunoreceptor tyrosine-based activation motifs) and ITIMs (immunoreceptor tyrosine-based inhibition motifs) that act as the receptors' interface with activating and inhibitory signaling pathways, respectively. While ITAMs mobilize activating tyrosine kinases and their consorts, ITIMs mobilize opposing tyrosine and inositol-lipid phosphatases. In this review, we will discuss our current understanding of signaling by these receptors/motifs and their sometimes blurred lines of function.

  14. Exploitation of peptide motif sequences and their use in nanobiotechnology.

    Science.gov (United States)

    Shiba, Kiyotaka

    2010-08-01

    Short amino acid sequences extracted from natural proteins or created using in vitro evolution systems are sometimes associated with particular biological functions. These peptides, called peptide motifs, can serve as functional units for the creation of various tools for nanobiotechnology. In particular, peptide motifs that have the ability to specifically recognize the surfaces of solid materials and to mineralize certain inorganic materials have been linking biological science to material science. Here, I review how these peptide motifs have been isolated from natural proteins or created using in vitro evolution systems, and how they have been used in the nanobiotechnology field.

  15. A comprehensive search for recombinogenic motifs in the human genome.

    Directory of Open Access Journals (Sweden)

    Henry R Johnston

    Full Text Available The patterns of male and female recombination vary greatly on a macro scale. A unique motif in each gender, triggering a double strand break at its location, much in the way Chi sites operate in E. coli, could logically explain this difference. As such, we have undertaken a comprehensive search of all small motifs in an attempt to identify one or more that match to the available data. In the end, we conclude that no such motifs appear to exist in the human genome.

  16. Identification of protein superfamily from structure- based sequence motif

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The structure-based sequence motif of the distant proteins in evolution, protein tyrosine phosphatases (PTP) Ⅰ and Ⅱ superfamilies, as an example, has been defined by the structural comparison, structure-based sequence alignment and analyses on substitution patterns of residues in common sequence conserved regions. And the phosphatases Ⅰ and Ⅱ can be correctly identified together by the structure-based PTP sequence motif from SWISS-PROT and TrEBML databases. The results show that the correct rates of identification are over 98%. This is the first time to identify PTP Ⅰ and Ⅱ together by this motif.

  17. ROMANIAN FOLKLORE MOTIFS IN FASHION DESIGN

    Directory of Open Access Journals (Sweden)

    MOCENCO Alexandra

    2014-05-01

    Full Text Available The traditional Romanian costume such as the entire popular art (architecture, woodcarvins, pottery etc. was born and lasted in our country since ancient times. Closely related to human existence, the traditional costume reflected over the years as reflected nowadays, the mentality and artistic conception of the people. Today the traditional Romanian costume became an inspiration source to the wholesale fashion production industry designers, both Romanian and international. Although the contemporary designers are working in accordance with a vision, using a wide area of styles, methods and current technology, they usually return to traditional techniques and ethnic folklore motifs, which converts and resize them, integrating them in their contemporary space. Adrian Oianu is a very appreciated Romanian designer who launched two collections inspired by his native’s country traditional costumes: “Suflecata pan’ la brau” (“Turned up ‘til the belt” and “Bucurie” (“Joy”. Dorin Negrau had as inspiration for his “Lost” collection the traditional costume from the Bihor region. Yves Saint Laurent had a collection inspired by the Romanian traditional flax blouses called “La blouse roumaine”. The paper presents the traditional Romanian values throw fashion collections. The research activity will create innovative concepts to support the garment industry in order to develop their own brand and to bring the design activities in Romania at an international level. The research was conducted during the initial stage of a project, financed through national founds, consisting in a documentary study on ethnographic characteristics of the popular costume from different regions of the country.

  18. Targeting functional motifs of a protein family

    Science.gov (United States)

    Bhadola, Pradeep; Deo, Nivedita

    2016-10-01

    The structural organization of a protein family is investigated by devising a method based on the random matrix theory (RMT), which uses the physiochemical properties of the amino acid with multiple sequence alignment. A graphical method to represent protein sequences using physiochemical properties is devised that gives a fast, easy, and informative way of comparing the evolutionary distances between protein sequences. A correlation matrix associated with each property is calculated, where the noise reduction and information filtering is done using RMT involving an ensemble of Wishart matrices. The analysis of the eigenvalue statistics of the correlation matrix for the β -lactamase family shows the universal features as observed in the Gaussian orthogonal ensemble (GOE). The property-based approach captures the short- as well as the long-range correlation (approximately following GOE) between the eigenvalues, whereas the previous approach (treating amino acids as characters) gives the usual short-range correlations, while the long-range correlations are the same as that of an uncorrelated series. The distribution of the eigenvector components for the eigenvalues outside the bulk (RMT bound) deviates significantly from RMT observations and contains important information about the system. The information content of each eigenvector of the correlation matrix is quantified by introducing an entropic estimate, which shows that for the β -lactamase family the smallest eigenvectors (low eigenmodes) are highly localized as well as informative. These small eigenvectors when processed gives clusters involving positions that have well-defined biological and structural importance matching with experiments. The approach is crucial for the recognition of structural motifs as shown in β -lactamase (and other families) and selectively identifies the important positions for targets to deactivate (activate) the enzymatic actions.

  19. An iron-catalysed C-C bond-forming spirocyclization cascade providing sustainable access to new 3D heterocyclic frameworks

    Science.gov (United States)

    Adams, Kirsty; Ball, Anthony K.; Birkett, James; Brown, Lee; Chappell, Ben; Gill, Duncan M.; Lo, P. K. Tony; Patmore, Nathan J.; Rice, Craig. R.; Ryan, James; Raubo, Piotr; Sweeney, Joseph B.

    2016-12-01

    Heterocyclic architectures offer powerful creative possibilities to a range of chemistry end-users. This is particularly true of heterocycles containing a high proportion of sp3-carbon atoms, which confer precise spatial definition upon chemical probes, drug substances, chiral monomers and the like. Nonetheless, simple catalytic routes to new heterocyclic cores are infrequently reported, and methods making use of biomass-accessible starting materials are also rare. Here, we demonstrate a new method allowing rapid entry to spirocyclic bis-heterocycles, in which inexpensive iron(III) catalysts mediate a highly stereoselective C-C bond-forming cyclization cascade reaction using (2-halo)aryl ethers and amines constructed using feedstock chemicals readily available from plant sources. Fe(acac)3 mediates the deiodinative cyclization of (2-halo)aryloxy furfuranyl ethers, followed by capture of the intermediate metal species by Grignard reagents, to deliver spirocycles containing two asymmetric centres. The reactions offer potential entry to key structural motifs present in bioactive natural products.

  20. The most common mutation of KRT9, c.C487T (p.R163W), in epidermolytic palmoplantar keratoderma in two large Chinese pedigrees.

    Science.gov (United States)

    Liu, Wen-Ting; Ke, Hai-Ping; Zhao, Yan; Chen, Xiao-Ling; Lu, Jia-Jun; Du, Zheng-Fang; Yu, Dan; Zhang, Xian-Ning

    2012-04-01

    Epidermolytic palmoplantar keratoderma (EPPK) is generally associated with dominant-negative mutations of the Keratin 9 gene (KRT9), and rarely with the Keratin 1 gene (KRT1). To date, a myriad of mutations has been reported with a high frequency of codon 163 mutations within the first exon of KRT9 in different populations. Notably, a distinct phenotypic heterogeneity, digital mutilation, was found recently in a 58-year-old female Japanese EPPK patient with p.R163W. Here, we report the most common mutation, c.C487T (p.R163W) of KRT9, in two large EPPK pedigrees from southeast China. The arginine residue in peptide position 163 remains almost constant in at least 47 intermediate filament proteins ranging from snail to human. A substitution in arginine alters both the charge and shape of the 1A rod domain and disrupts the function of the helix initiation motif of keratins, finally compromising the integrity of filaments and weakening their stability in the epidermis of palms and soles. We summarize the clinical symptoms of EPPK in Chinese and show that knuckle pads are associated with KRT9 mutations. We suggest that the frequency of p.R163W in Chinese EPPK patients (31.03%) is consistent with that in the general population (29.33%), and that codon 163 is truly a hotspot mutational site of KRT9.

  1. Long-term tropospheric trend of octafluorocyclobutane (c-C4F8 or PFC-318

    Directory of Open Access Journals (Sweden)

    T. Röckmann

    2011-07-01

    Full Text Available Air samples collected at Cape Grim, Tasmania between 1978 and 2008 and during a series of more recent aircraft sampling programmes have been analysed to determine the atmospheric abundance and trend of octafluorocyclobutane (-C4F8 or PFC-318. c-C4F8 has an atmospheric lifetime in excess of 3000 yr and a global warming potential (GWP of 10 300 (100 yr time horizon, making it one of the most potent greenhouse gases detected in the atmosphere to date. The abundance of c-C4F8 in the Southern Hemisphere has risen from 0.35 ppt in 1978 to 1.2 ppt in 2010, and is currently increasing at a rate of around 0.03 ppt yr−1. It is the third most abundant perfluorocarbon (PFC in the present day atmosphere, behind CF4 (~75 ppt and C2F6 (~4 ppt. The origin of c-C4F8 is unclear. Using a 2-D global model to derive top-down global emissions based on the Cape Grim measurements yields a recent (2007 emission rate of around 1.1 Gg yr−1 and a cumulative emission up to and including 2007 of 38.1 Gg. Emissions reported on the EDGAR emissions database for the period 1986–2005 represent less than 1 % of the top-down emissions for the same period, which suggests there is a large unaccounted for source of this compound. It is also apparent that the magnitude of this source has varied considerably over the past 30 yr, declining sharply in the late 1980s before increasing again in the mid-1990s.

  2. Structure of Leptin Receptor Related with Obesity

    DEFF Research Database (Denmark)

    Toleikis, Zigmantas

    The hormone leptin is central to obesity, but the molecular processes underlying the activation of the leptin receptor are unknown. To further the understanding of the system, an atomic resolution structure of this cytokine type I receptor in the unbound inactive form and in the activated bound...... of the receptor, while the D5 domain is the central leptin-binding domain, implicated in the first steps of activation. Both domains are characterized by a fibronectin type III fold and both contain a conserved WSXWS motif (X represents an unconserved amino acid residue), a distinct feature of the cytokine...... receptors. This motif is thought to play a major role in correct folding and activation of the receptor. The complex between leptin and the D5CA domain was analyzed using nuclear magnetic resonance spectroscopy and the amino acid residues implicated in the binding were determined. To investigate which parts...

  3. Measurement of Swarm Parameters of c-C4F8/CO2 and Its Insulation Characteristics Analysis

    Institute of Scientific and Technical Information of China (English)

    ZHANG Liu-chun; XIAO Deng-ming; ZHANG Dong; WU Bian-tao

    2008-01-01

    In c-C4F8 and c-C4F8/CO2 mixtures, the swarm parameters including ionization coefficient, attachment coefficient and effective ionization coefficient were obtained at the ratio of the electric field strength to the gas density between 150-550 Td by the steady-state Townsend (SST) method. Static breakdown voltages at each ratio were also measured at the SST condition. The limiting field strengths were obtained by two methods:computing the density-normalized effective ionization coefficient as a function of the overall density-reduced electric field strength; and measuring static breakdown voltages as a function of the product of gas density and electrode separation. Good agreement was obtained by these two methods, which ensures the correctness of the former method. The limiting field strengths of c-C4F8 and c-C4F8/CO2 mixtures were compared with those ofpure SF6, SF6/CO2 mixtures and pure c-C4Fs. It is found that buffer gas CO2 does not reduce the limiting field strengths of c-C4F8 greatly, the limiting field strengths of c-C4F8/CO2 mixtures are higher than those of SF6/CO2 mixtures or even pure SF6, and so c-C4F8/CO2 mixtures are suggested to be possible substitutes for SF6.

  4. The large 1 1Ag - 2 1Ag C=C stretching vibronic interaction in all-trans polyenes

    NARCIS (Netherlands)

    Buma, W.J.; Zerbetto, F.

    1998-01-01

    An ab initio theoretical approach at several levels of theory is employed to calculate the 11Ag--21Ag- (non)adiabatic vibronic couplings induced by the completely in-phase C=C and C-C bond stretching vibrations of five all-trans polyenes (from butadiene to dodecahexaene). The nonadiabatic couplings

  5. 77 FR 12578 - Notice of Intent To Grant Exclusive Patent License; C&C Ventures, Doing Business as Randolph...

    Science.gov (United States)

    2012-03-01

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF DEFENSE Department of the Navy Notice of Intent To Grant Exclusive Patent License; C&C Ventures, Doing Business as... hereby gives notice of its intent to grant to C&C Ventures, doing business as Randolph Products,...

  6. Charged pion production in C+C and Ar+KCl collisions measured with HADES

    CERN Document Server

    Tlustý, P; Balanda, A; Bellia, G; Belver, D; Belyaev, A; Blanco, A; Boehmer, M; Boyard, J L; Braun-Munzinger, P; Cabanelas, P; Castro, E; Chernenko, S; Christ, T; Destefanis, M; Díaz, J; Dohrmann, F; Dybczak, A; Fabbietti, L; Fateev, O; Finocchiaro, P; Fonte, P; Friese, J; Fröhlich, I; Galatyuk, T; Garzón, J A; Gernhäuser, R; Gil, A; Gilardi, C; Golubeva, M; Gonzalez-Diaz, D; Grosse, E; Guber, F; Heilmann, M; Hennino, T; Holzmann, R; Ierusalimov, A; Iori, I; Ivashkin, A; Jurkovic, M; Kämpfer, B; Kanaki, K; Karavicheva, T; Kirschner, D; König, I; König, W; Kolb, B W; Kotte, R; Kozuch, A; Krasa, A; Krizek, F; Krücken, R; Kühn, W; Kugler, A; Kurepin, A; Lamas-Valverde, J; Lang, S; Lange, J S; Lapidus, K; Liu, T; Lopes, L; Lorenz, M; Maier, L; Mangiarotti, A; Marin, J; Markert, J; Metag, V; Michalska, B; Michel, J; Mishra, D; Moriniere, E; Mousa, J; Müntz, C; Naumann, L; Novotny, R; Otwinowski, J; Pachmayer, Y C; Palka, M; Parpottas, Y; Pechenov, V; Pechenova, O; Cavalcanti, T Perez; Pietraszko, J; Przygoda, W; Ramstein, B; Reshetin, A; Rustamov, A; Sadovskii, A; Salabura, P; Schmah, A; Simon, R; Sobolev, Yu G; Spataro, S; Spruck, B; Ströbele, H; Stroth, J; Sturm, C; Sudol, M; Tarantola, A; Teilab, K; Traxler, M; Trebacz, R; Tsertos, H; Veretenkin, I; Wagner, V; Weber, M; Wisniowski, M; Wüstenfeld, J; Yurevich, S; Zanevsky, Y; Zhou, P; Zumbruch, P

    2009-01-01

    Results of a study of charged pion production in 12C+12C collisions at incident beam energies of 1A GeV and 2A GeV, and 40Ar+natKCl at 1.76AGeV, using the spectrometer HADES at GSI, are presented. We have performed a measurement of the transverse momentum distributions of pi+- mesons covering a fairly large rapidity interval, in case of the C+C collision system for the first time. The yields, transverse mass and angular distributions are compared with a transport model as well as with existing data from other experiments.

  7. Study of dielectron production in C+C collisions at 1 AGeV

    CERN Document Server

    Agakichiev, G; Pol, H Alvarez; Balanda, A; Bassini, R; Bellia, G; Belver, D; Belyaev, A; Blanco, A; Boehmer, M; Bortolotti, A; Boyard, J L; Braun-Munzinger, P; Cabanelas, P; Castro, E; Christ, T; Destefanis, M; Díaz, J; Dohrmann, F; Dybczak, A; Eberl, T; Fabbietti, L; Finocchiaro, P; Fonte, Paulo J R; Friese, J; Fröhlich, I; Galatyuk, T; Garzón, J A; Gernhäuser, R; Gil, A; Gilardi, C; Golubeva, M; Diaz, D Gonzalez; Grosse, E; Guber, F; Heilmann, M; Hennino, T; Holzmann, R; Ierusalimov, A; Iori, I; Ivashkin, A; Jurkovic, M; Kämpfer, B; Kanaki, K; Karavicheva, T; Kirschner, D; König, I; König, W; Kolb, B W; Kotte, R; Kozuch, A; Krasa, A; Krizek, F; Krücken, R; Kühn, W; Kugler, A; Kurepin, A; Valverde, J Lamas; Lang, S; Lange, J S; Lapidus, K; Lopes, L; Maier, L; Mangiarotti, A; Marin, J; Markert, J; Metag, V; Michalska, B; Mishra, D; Moriniere, E; Mousa, J; Münch, M; Müntz, C; Naumann, Lutz; Novotny, R; Otwinowski, J; Pachmayer, Y C; Palka, M; Parpottas, Y; Pechenov, V; Pechenova, O; Perez, T; Pietraszko, J; Pleskac, R; Przygoda, W; Ramstein, B; Reshetin, A; Stephan, M Roy; Rustamov, A; Sadovskii, A; Sailer, B; Salabura, P; Schmah, A; Simon, R; Sobolev, Y; Spataro, S; Spruck, B; Ströbele, H; Stroth, J; Sturm, C; Sudol, M; Tarantola, A; Teilab, K; Tlustý, P; Toia, A; Traxler, M; Trebacz, R; Tsertos, H; Veretenkin, I; Wagner, V; Weber, M; Wen, H; Wisniowski, M; Wojcik, T; Wüstenfeld, J; Yurevich, S; Zanevsky, Y; Zhou, P; Zumbruch, P

    2007-01-01

    The emission of e+e- pairs from C+C collisions at an incident energy of 1 GeV per nucleon has been investigated. The measured production probabilities, spanning from the pi0-Dalitz to the rho/omega! invariant-mass region, display a strong excess above the cocktail of standard hadronic sources. The bombarding-energy dependence of this excess is found to scale like pion production, rather than like eta production. The data are in good agreement with results obtained in the former DLS experiment.

  8. An erbium-based bifuctional heterogeneous catalyst: a cooperative route towards C-C bond formation.

    Science.gov (United States)

    Oliverio, Manuela; Costanzo, Paola; Macario, Anastasia; De Luca, Giuseppina; Nardi, Monica; Procopio, Antonio

    2014-07-15

    Heterogeneous bifuctional catalysts are multifunctional synthetic catalysts enabling efficient organic transformations by exploiting two opposite functionalities without mutual destruction. In this paper we report the first Er(III)-based metallorganic heterogeneous catalyst, synthesized by post-calcination MW-assisted grafting and modification of the natural aminoacid L-cysteine. The natural acid-base distance between sites was maintained to assure the cooperation. The applicability of this new bifunctional heterogeneous catalyst to C-C bond formation and the supposed mechanisms of action are discussed as well.

  9. Microanalysis on the Hydrogen Ion Irradiated 50 wt pct TiC-C Films

    Institute of Scientific and Technical Information of China (English)

    Hui JIANG; Yaoguang LIU; Ningkang HUANG

    2007-01-01

    The 50 wt pct TiC-C films were prepared on stainless steel substrates by using a technique of ion beam mixing.These films were irradiated by hydrogen ion beam with a dose of 1×1018 ions/cm2 and an energy of 5 keV.Microanalysis of X-ray photoelectron spectroscopy (XPS) and secondary ion mass spectroscopy (SIMS) were used to analyze the films before and after hydrogen ion irradiation and to study the mechanism of hydrogen resistance.

  10. Homolytic Bond Dissociation Enthalpies of C C and C-H Bonds in Highly Crowded Alkanes

    Institute of Scientific and Technical Information of China (English)

    ZHU Chen; RUI Lei; FU Yao

    2008-01-01

    The homolytic C-C and C--H bond dissociation enthalpyies (BDE) of highly crowded alkanes were calcu- lated by using an ONIOM-G3B3 method. Geometric parameters such as bond length, bond angle and molecular volume were carefully investigated, as most of the acyclic alkanes in this study were not yet synthesized. These pa-rameters reflect the influence of steric effect on BDE. Good correlations were found between the rapid decrease of BDE and the increase of molecular volumes. The correlations can be applied to the prediction of the possible exis-tence of many highly strained compounds.

  11. An Erbium-Based Bifuctional Heterogeneous Catalyst: A Cooperative Route Towards C-C Bond Formation

    Directory of Open Access Journals (Sweden)

    Manuela Oliverio

    2014-07-01

    Full Text Available Heterogeneous bifuctional catalysts are multifunctional synthetic catalysts enabling efficient organic transformations by exploiting two opposite functionalities without mutual destruction. In this paper we report the first Er(III-based metallorganic heterogeneous catalyst, synthesized by post-calcination MW-assisted grafting and modification of the natural aminoacid L-cysteine. The natural acid–base distance between sites was maintained to assure the cooperation. The applicability of this new bifunctional heterogeneous catalyst to C-C bond formation and the supposed mechanisms of action are discussed as well.

  12. Activation of Aromatic C-C Bonds of 2,2'-Bipyridine Ligands.

    Science.gov (United States)

    Fombona, Sergio; Espinal-Viguri, Maialen; Huertos, Miguel A; Díaz, Jesús; López, Ramón; Menéndez, M Isabel; Pérez, Julio; Riera, Lucía

    2016-11-21

    4,4'-Disubstituted-2,2'-bipyridine ligands coordinated to Mo(II) and Re(I) cationic fragments become dearomatized by an intramolecular nucleophilic attack from a deprotonated N-alkylimidazole ligand in cis disposition. The subsequent protonation of these neutral complexes takes place on a pyridine carbon atom rather than at nitrogen, weakening an aromatic C-C bond and affording a dihydropyridyl moiety. Computational calculations allowed for the rationalization of the formation of the experimentally obtained products over other plausible alternatives.

  13. An autoinhibited conformation of LGN reveals a distinct interaction mode between GoLoco motifs and TPR motifs.

    Science.gov (United States)

    Pan, Zhu; Zhu, Jinwei; Shang, Yuan; Wei, Zhiyi; Jia, Min; Xia, Caihao; Wen, Wenyu; Wang, Wenning; Zhang, Mingjie

    2013-06-01

    LGN plays essential roles in asymmetric cell divisions via its N-terminal TPR-motif-mediated binding to mInsc and NuMA. This scaffolding activity requires the release of the autoinhibited conformation of LGN by binding of Gα(i) to its C-terminal GoLoco (GL) motifs. The interaction between the GL and TPR motifs of LGN represents a distinct GL/target binding mode with an unknown mechanism. Here, we show that two consecutive GL motifs of LGN form a minimal TPR-motif-binding unit. GL12 and GL34 bind to TPR0-3 and TPR4-7, respectively. The crystal structure of a truncated LGN reveals that GL34 forms a pair of parallel α helices and binds to the concave surface of TPR4-7, thereby preventing LGN from binding to other targets. Importantly, the GLs bind to TPR motifs with a mode distinct from that observed in the GL/Gα(i)·GDP complexes. Our results also indicate that multiple and orphan GL motif proteins likely respond to G proteins with distinct mechanisms.

  14. Review article: The mountain motif in the plot of Matthew

    Directory of Open Access Journals (Sweden)

    Gert J. Volschenk

    2010-02-01

    Full Text Available This article reviewed T.L. Donaldson’s book, Jesus on the mountain: A study in Matthean theology, published in 1985 by JSOT Press, Sheffield, and focused on the mountain motif in the structure and plot of the Gospel of Matthew, in addition to the work of Donaldson on the mountain motif as a literary motif and as theological symbol. The mountain is a primary theological setting for Jesus’ ministry and thus is an important setting, serving as one of the literary devices by which Matthew structured and progressed his narrative. The Zion theological and eschatological significance and Second Temple Judaism serve as the historical and theological background for the mountain motif. The last mountain setting (Mt 28:16–20 is the culmination of the three theological themes in the plot of Matthew, namely Christology, ecclesiology and salvation history.

  15. Tribological properties of C/C-SiC composites for brake discs

    Science.gov (United States)

    Jang, G. H.; Cho, K. H.; Park, S. B.; Lee, W. G.; Hong, U. S.; Jang, H.

    2010-02-01

    This study examines the friction and wear of ceramic matrix composites designed for use in automotive brake discs. The composites are produced by reinforcing a SiC matrix with carbon fibers using a liquid silicon infiltration method. C/C-SiC composites with two different compositions are fabricated to examine the compositional effect on the tribological properties. The tribological properties are evaluated using a scale dynamometer with a low-steel type friction material. The results show that the coefficient of friction is determined by the composition of the composite, which affects the propensity of friction film formation on the disc surface. A stable friction film on the disc surface also improves the wear resistance by diminishing the abrasive action of the disc. On the other hand, the friction film formation on the disc is affected by the applied pressure, and stable films are obtained at high pressures. This trend is prominent with discs with high Si content. However, both C/C/-SiC composites show superior performance in terms of the friction force oscillation, which is closely related to brake-induced vibration.

  16. Effect of Treated Graphite on Properties of Al2 O3-SiC-C Castables

    Institute of Scientific and Technical Information of China (English)

    SHI Huiying; ZHANG Yang; BU Xiangjuan; CAO Xiying; HE Jiasong; WANG Lei

    2009-01-01

    Al2O3-SiC-C castables with 2 % pitch or 2 %,4% and 6% treated graphite,respectively,were prepared based on the basic formulation of traditional Al2O3-SiC-C castables.The flowability of castables,and bulk density,volume stability,strength,oxidation resistance and slag resistance of specimens fired at 110 ℃,1 100 ℃ and 1 500 ℃ respectively were comparatively studied.The results showed that:(1) With carbon source changing from pitch to treated graphite and the increase of treated graphite addition,water addition of castables increased,bulk density of specimens fired at different temperatures increased firstly and then decreased,strength after drying decreased obviously,strength after firing and oxidation resistance changed slightly,hot modulus of rupture increased obviously;(2) Slag resistance of specimen with treated graphite was worse than that of specimen with the same amount of pitch,but the former was obviously improved with the increase of treated graphite addition.

  17. Benefits of X-Ray CMT for the modeling of C/C composites

    Energy Technology Data Exchange (ETDEWEB)

    Coindreau, Olivia; Lachaud, Jean; Vignoles, Gerard L. [LCTS - UMR 5801 CNRS-Universite Bordeaux 1-Safran-CEA 3, Allee La Boetie, Pessac, F33600 (France); Mulat, Christianne [LCTS - UMR 5801 CNRS-Universite Bordeaux 1-Safran-CEA 3, Allee La Boetie, Pessac, F33600 (France); IMS - UMR5218 CNRS-Universite Bordeaux 1-IPB 351, Avenue de la Liberation, Talence, F33410 (France); Germain, Christian [IMS - UMR5218 CNRS-Universite Bordeaux 1-IPB 351, Avenue de la Liberation, Talence, F33410 (France)

    2011-03-15

    C/C composites have application in very demanding areas like aerospace, fusion technology, etc. and thus their optimization is crucial, both in the control of processing routes and in the prediction of their behavior in use. Intense modeling efforts have been performed in these directions. To help a direct application on actual materials, with possibly complex reinforcement architectures, X-ray computerized micro-tomography (CMT) is a beneficial technique, since it allows producing extremely detailed representations of these architectures. However, there is a long way from the crude X-ray projections to the information that is directly usable in C/C composite modeling. This paper summarizes several achievements in this domain and discusses the obtained results, concerning (i) composites imaging by phase contrast CMT and holographic CMT, (ii) evaluation of effective geometrical and transfer properties in fiber arrangements and actual fiber-reinforced composites, (iii) modeling of degradation by ablation, and (iv) modeling of processing by chemical vapor infiltration. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  18. Molecular dynamics prediction of phonon-mediated thermal conductivity of f.c.c. Cu

    Science.gov (United States)

    Evteev, Alexander V.; Momenzadeh, Leila; Levchenko, Elena V.; Belova, Irina V.; Murch, Graeme E.

    2014-03-01

    The phonon-mediated thermal conductivity of f.c.c. Cu is investigated in detail in the temperature range 40-1300 K. The calculations are performed in the framework of equilibrium molecular dynamics making use of the Green-Kubo formalism and one of the most reliable embedded-atom method potentials for Cu. It is found that the temporal decay of the heat current autocorrelation function (HCACF) of the Cu model at low and intermediate temperatures demonstrate a more complex behaviour than the two-stage decay observed previously for the f.c.c. Ar model. After the first stage of decay, it demonstrates a peak in the temperature range 40-800 K. A decomposition model of the HCACF is introduced. In the framework of that model we demonstrate that a classical description of the phonon thermal transport in the Cu model can be used down to around one quarter of the Debye temperature (about 90 K). Also, we find that above 300 K the thermal conductivity of the Cu model varies with temperature more rapidly than ?, following an exponent close to -1.4 in agreement with previous calculations on the Ar model. Phonon thermal conductivity of Cu is found to be about one order of magnitude higher than Ar. The phonon contribution to the total thermal conductivity of Cu can be estimated to be about 0.5% at 1300 K and about 10% at 90 K.

  19. The Origin of Motif Families in Food Webs

    OpenAIRE

    Klaise, Janis; Johnson, Samuel

    2016-01-01

    Food webs have been found to exhibit remarkable motif profiles, patterns in the relative prevalences of all possible three-species sub-graphs, and this has been related to ecosystem properties such as stability and robustness. Analysing 46 food webs of various kinds, we find that most food webs fall into one of two distinct motif families. The separation between the families is well predicted by a global measure of hierarchical order in directed networks - trophic coherence. We find that trop...

  20. Robust and Adaptive MicroRNA-Mediated Incoherent Feedforward Motifs

    Institute of Scientific and Technical Information of China (English)

    XU Feng-Dan; LIU Zeng-Rong; ZHANG Zhi-Yong; SHEN Jian-Wei

    2009-01-01

    We integrate transcriptional and post-transcriptional regulation into microRNA-mediated incoherent feedforward motifs and analyse their dynamical behaviour and functions. The analysis show that the behaviour of the system is almost uninfluenced by the varying input in certain ranges and by introducing of delay and noise. The results indicate that microRNA-mediated incoherent feedforward motifs greatly enhance the robustness of gene regulation.

  1. Three-Dimensional DNA Nanostructures Assembled from DNA Star Motifs.

    Science.gov (United States)

    Tian, Cheng; Zhang, Chuan

    2017-01-01

    Tile-based DNA self-assembly is a promising method in DNA nanotechnology and has produced a wide range of nanostructures by using a small set of unique DNA strands. DNA star motif, as one of DNA tiles, has been employed to assemble varieties of symmetric one-, two-, three-dimensional (1, 2, 3D) DNA nanostructures. Herein, we describe the design principles, assembly methods, and characterization methods of 3D DNA nanostructures assembled from the DNA star motifs.

  2. A dileucine motif is involved in plasma membrane expression and endocytosis of rat sodium taurocholate cotransporting polypeptide (Ntcp).

    Science.gov (United States)

    Stross, Claudia; Kluge, Stefanie; Weissenberger, Katrin; Winands, Elisabeth; Häussinger, Dieter; Kubitz, Ralf

    2013-11-15

    The sodium taurocholate cotransporting polypeptide (Ntcp) is the major uptake transporter for bile salts into liver parenchymal cells, and PKC-mediated endocytosis was shown to regulate the number of Ntcp molecules at the plasma membrane. In this study, mechanisms of Ntcp internalization were analyzed by flow cytometry, immunofluorescence, and Western blot analyses in HepG2 cells. PKC activation induced endocytosis of Ntcp from the plasma membrane by ~30%. Endocytosis of Ntcp was clathrin dependent and was followed by lysosomal degradation. A dileucine motif located in the third intracellular loop of Ntcp was essential for endocytosis but also for processing and plasma membrane targeting, suggesting a dual function of this motif for intracellular trafficking of Ntcp. Mutation of two of five potential phosphorylation sites surrounding the dileucine motif (Thr225 and Ser226) inhibited PKC-mediated endocytosis. In conclusion, we could identify a motif, which is critical for Ntcp plasma membrane localization. Endocytic retrieval protects hepatocytes from elevated bile salt concentrations and is of special interest, because NTCP has been identified as a receptor for the hepatitis B and D virus.

  3. Would be the photon a composed particle? / Sobre a possibilidade da quantiza\\c{c}\\~ao dos fluxos de campo na radia\\c{c}\\~ao eletromagn\\'etica

    CERN Document Server

    Duarte, Celso de Araujo

    2013-01-01

    Here it is made a comparative analysis between the classical and the quantum expressions for the energy of electromagnetic radiation (ER). The comparison points to the possibility of the quantization of the magnetic and the electric field fluxes in the ER. ----- Apresenta-se uma an\\'alise comparativa entre as express\\~oes cl\\'assica e qu\\^antica para a energia da radia\\c{c}\\~ao eletromagn\\'etica (RE). A compara\\c{c}\\~ao nos aponta para a possibilidade de haver uma quantiza\\c{c}\\~ao dos fluxos dos campos magn\\'etico e el\\'etrico na RE.

  4. Efficient motif finding algorithms for large-alphabet inputs

    Directory of Open Access Journals (Sweden)

    Pavlovic Vladimir

    2010-10-01

    Full Text Available Abstract Background We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are embedded as exact or inexact instances in all or most of the input strings. Results The proposed algorithm (1 improves search efficiency compared to existing algorithms, and (2 scales well with the size of alphabet. On a synthetic planted DNA motif finding problem our algorithm is over 10× more efficient than MITRA, PMSPrune, and RISOTTO for long motifs. Improvements are orders of magnitude higher in the same setting with large alphabets. On benchmark TF-binding site problems (FNP, CRP, LexA we observed reduction in running time of over 12×, with high detection accuracy. The algorithm was also successful in rapidly identifying protein motifs in Lipocalin, Zinc metallopeptidase, and supersecondary structure motifs for Cadherin and Immunoglobin families. Conclusions Our algorithm reduces computational complexity of the current motif finding algorithms and demonstrate strong running time improvements over existing exact algorithms, especially in important and difficult cases of large-alphabet sequences.

  5. Transcriptional Network Growing Models Using Motif-Based Preferential Attachment.

    Science.gov (United States)

    Abdelzaher, Ahmed F; Al-Musawi, Ahmad F; Ghosh, Preetam; Mayo, Michael L; Perkins, Edward J

    2015-01-01

    Understanding relationships between architectural properties of gene-regulatory networks (GRNs) has been one of the major goals in systems biology and bioinformatics, as it can provide insights into, e.g., disease dynamics and drug development. Such GRNs are characterized by their scale-free degree distributions and existence of network motifs - i.e., small-node subgraphs that occur more abundantly in GRNs than expected from chance alone. Because these transcriptional modules represent "building blocks" of complex networks and exhibit a wide range of functional and dynamical properties, they may contribute to the remarkable robustness and dynamical stability associated with the whole of GRNs. Here, we developed network-construction models to better understand this relationship, which produce randomized GRNs by using transcriptional motifs as the fundamental growth unit in contrast to other methods that construct similar networks on a node-by-node basis. Because this model produces networks with a prescribed lower bound on the number of choice transcriptional motifs (e.g., downlinks, feed-forward loops), its fidelity to the motif distributions observed in model organisms represents an improvement over existing methods, which we validated by contrasting their resultant motif and degree distributions against existing network-growth models and data from the model organism of the bacterium Escherichia coli. These models may therefore serve as novel testbeds for further elucidating relationships between the topology of transcriptional motifs and network-wide dynamical properties.

  6. Transcriptional Network growing Models using Motif-based Preferential Attachment

    Directory of Open Access Journals (Sweden)

    Ahmed Farouk Abdelzaher

    2015-10-01

    Full Text Available Understanding relationships between architectural properties of gene-regulatory networks (GRNs has been one of the major goals in systems biology and bioinformatics, as it can provide insights into, e.g., disease dynamics and drug development. Such GRNs are characterized by their scale-free degree distributions and existence of network motifs--i.e., small-node subgraphs that occur more abundantly in GRNs than expected from chance alone. Because these transcriptional modules represent ``building blocks'' of complex networks and exhibit a wide range of functional and dynamical properties, they may contribute to the remarkable robustness and dynamical stability associated with the whole of GRNs. Here we developed network-construction models to better understand this relationship, which produce randomized GRNs by using transcriptional motifs as the fundamental growth unit in contrast to other methods that construct similar networks on a node-by-node basis. Because this model produces networks with a prescribed lower bound on the number of choice transcriptional motifs (e.g., downlinks, feed-forward loops, its fidelity to the motif distributions observed in model organisms represents an improvement over existing methods, which we validated by contrasting their resultant motif and degree distributions against existing network-growth models and data from the model organism of the bacterium Escherichia coli. These models may therefore serve as novel testbeds for further elucidating relationships between the topology of transcriptional motifs and network-wide dynamical properties.

  7. The distribution of RNA motifs in natural sequences.

    Science.gov (United States)

    Bourdeau, V; Ferbeyre, G; Pageau, M; Paquin, B; Cedergren, R

    1999-11-15

    Functional analysis of genome sequences has largely ignored RNA genes and their structures. We introduce here the notion of 'ribonomics' to describe the search for the distribution of and eventually the determination of the physiological roles of these RNA structures found in the sequence databases. The utility of this approach is illustrated here by the identification in the GenBank database of RNA motifs having known binding or chemical activity. The frequency of these motifs indicates that most have originated from evolutionary drift and are selectively neutral. On the other hand, their distribution among species and their location within genes suggest that the destiny of these motifs may be more elaborate. For example, the hammerhead motif has a skewed organismal presence, is phylogenetically stable and recent work on a schistosome version confirms its in vivo biological activity. The under-representation of the valine-binding motif and the Rev-binding element in GenBank hints at a detrimental effect on cell growth or viability. Data on the presence and the location of these motifs may provide critical guidance in the design of experiments directed towards the understanding and the manipulation of RNA complexes and activities in vivo.

  8. A sialoreceptor binding motif in the Mycoplasma synoviae adhesin VlhA.

    Directory of Open Access Journals (Sweden)

    Meghan May

    Full Text Available Mycoplasma synoviae depends on its adhesin VlhA to mediate cytadherence to sialylated host cell receptors. Allelic variants of VlhA arise through recombination between an assemblage of promoterless vlhA pseudogenes and a single transcription promoter site, creating lineages of M. synoviae that each express a different vlhA allele. The predicted full-length VlhA sequences adjacent to the promoter of nine lineages of M. synoviae varying in avidity of cytadherence were aligned with that of the reference strain MS53 and with a 60-a.a. hemagglutinating VlhA C-terminal fragment from a Tunisian lineage of strain WVU1853(T. Seven different sequence variants of an imperfectly conserved, single-copy, 12-a.a. candidate cytadherence motif were evident amid the flanking variable residues of the 11 total sequences examined. The motif was predicted to adopt a short hairpin structure in a low-complexity region near the C-terminus of VlhA. Biotinylated synthetic oligopeptides representing four selected variants of the 12-a.a. motif, with the whole synthesized 60-a.a. fragment as a positive control, differed (P<0.01 in the extent they bound to chicken erythrocyte membranes. All bound to a greater extent (P<0.01 than scrambled or irrelevant VlhA domain negative control peptides did. Experimentally introduced branched-chain amino acid (BCAA substitutions Val3Ile and Leu7Ile did not significantly alter binding, whereas fold-destabilizing substitutions Thr4Gly and Ala9Gly tended to reduce it (P<0.05. Binding was also reduced to background levels (P<0.01 when the peptides were exposed to desialylated membranes, or were pre-saturated with free sialic acid before exposure to untreated membranes. From this evidence we conclude that the motif P-X-(BCAA-X-F-X-(BCAA-X-A-K-X-G binds sialic acid and likely mediates VlhA-dependent M. synoviae attachment to host cells. This conserved mechanism retains the potential for fine-scale rheostasis in binding avidity, which could be a

  9. Frequency patterns of T-cell exposed motifs in immunoglobulin heavy chain peptides presented by MHCs

    Directory of Open Access Journals (Sweden)

    Robert D. Bremel

    2014-10-01

    Full Text Available Immunoglobulins are highly diverse protein sequences that are processed and presented to T-cells by B-cells and other antigen presenting cells. We examined a large dataset of immunoglobulin heavy chain variable regions (IGHV to assess the diversity of T-cell exposed motifs (TCEM. TCEM comprise those amino acids in a MHC-bound peptide which face outwards, surrounded by the MHC histotope, and which engage the T-cell receptor. Within IGHV there is a distinct pattern of predicted MHC class II binding and a very high frequency of re-use of the TCEMs. The re-use frequency indicates that only a limited number of different cognate T-cells are required to engage many different clonal B-cells. The amino acids in each outward-facing TCEM are intercalated with the amino acids of inward-facing MHC groove-exposed motifs (GEM. Different GEM may have differing, allele-specific, MHC binding affinities. The intercalation of TCEM and GEM in a peptide allows for a vast combinatorial repertoire of epitopes, each eliciting a different response. Outcome of T-cell receptor binding is determined by overall signal strength, which is a function of the number of responding T-cells and the duration of engagement. Hence, the frequency of T-cell exposed motif re-use appears to be an important determinant of whether a T-cell response is stimulatory or suppressive. The frequency distribution of TCEMs implies that somatic hypermutation is followed by clonal expansion that develop along repeated pathways. The observations of TCEM and GEM derived from immunoglobulins suggest a relatively simple, yet powerful, mechanism to correlate T-cell polyspecificity, through re-use of TCEMs, with a very high degree of specificity achieved by combination with a diversity of GEMs. The frequency profile of TCEMs also points to an economical mechanism for maintaining T-cell memory, recall, and self-discrimination based on an endogenously generated profile of motifs.

  10. In silico analysis of molecular mechanisms of Galanthus nivalis agglutinin-related lectin-induced cancer cell death from carbohydrate-binding motif evolution hypothesis.

    Science.gov (United States)

    Yu, Qi-Jia; Li, Zi-Yue; Yao, Shun; Ming, Miao; Wang, Shu-Ya; Liu, Bo; Bao, Jin-Ku

    2011-10-01

    Galanthus nivalis agglutinin-related lectins, a superfamily of strictly mannose-binding-specific lectins widespread amongst monotyledonous plants, have drawn a rising attention for their remarkable anti-proliferative and apoptosis-inducing activities toward various types of cancer cells; however, the precise molecular mechanisms by which they induce tumor cell apoptosis are still only rudimentarily understood. Herein, we found that the three conserved motifs "QXDXNXVXY," the mannose-specific binding sites, could mutate at one or more amino acid sites, which might be a driving force for the sequential evolution and thus ultimately leading to the complete disappearance of the three conserved motifs. In addition, we found that the motif evolution could result in the diversification of sugar-binding types that G. nivalis agglutinin-related lectins could bind from specific mannose receptors to more types of sugar-containing receptors in cancer cells. Subsequently, we indicated that some sugar-containing receptors such as TNFR1, EGFR, Hsp90, and Hsp70 could block downstream anti-apoptotic or survival signaling pathways, which, in turn, resulted in tumor cell apoptosis. Taken together, our hypothesis that carbohydrate-binding motif evolution may impact the G. nivalis agglutinin-related lectin-induced survival or anti-apoptotic pathways would provide a new perspective for further elucidating the intricate relationships between the carbohydrate-binding specificities and complex molecular mechanisms by which G. nivalis agglutinin-related lectins induce cancer cell death.

  11. Preliminary Discussion on C/C++Program Design Course Teaching in Higher Vocational Colleges%浅谈高职院校C/C++程序设计课程教学

    Institute of Scientific and Technical Information of China (English)

    徐立艳

    2013-01-01

    The C/C++program design is a basic course of computer specialty. The course is difficult to teach and learn, perplexes largeness teachers and students. Based on analyzing many years of teaching experience, summarizing the problems in the course of teaching, and drawing aged teachers’teaching views, the author puts forward some sugges-tions on C/C++program design teaching.%C/C++程序设计是计算机专业的一门基础课程,该课程难教、难学一直困扰着广大师生,根据多年的教学经验,总结自己在教学过程中存在的问题,听取老教师的教学观点,提出C/C++程序设计教学的几点建议。

  12. Facile P-C/C-H Bond-Cleavage Reactivity of Nickel Bis(diphosphine) Complexes.

    Science.gov (United States)

    Zhang, Shaoguang; Li, Haixia; Appel, Aaron M; Hall, Michael B; Bullock, R Morris

    2016-07-04

    Unusual cleavage of P-C and C-H bonds of the P2 N2 ligand, in heteroleptic [Ni(P2 N2 )(diphosphine)](2+) complexes under mild conditions, results in the formation of an iminium formyl nickelate featuring a C,P,P-tridentate coordination mode. The structures of both the heteroleptic [Ni(P2 N2 )(diphosphine)](2+) complexes and the resulting iminium formyl nickelate have been characterized by NMR spectroscopy and single-crystal X-ray diffraction analysis. Density functional theory (DFT) calculations were employed to investigate the mechanism of the P-C/C-H bond cleavage, which involves C-H bond cleavage, hydride rotation, Ni-C/P-H bond formation, and P-C bond cleavage.

  13. Mesophase formation of coal-tar pitches used for impregnant of C/C composites

    Institute of Scientific and Technical Information of China (English)

    巩前明; 黄启忠; 黄伯云; 张福勤; 陈腾飞

    2001-01-01

    By a polarized light optical microscopy with a hot stage, liquid-phase nuclear magnetic resonance 13 C-NMR and 1 H-NMR, X-ray diffractometry and scanning electron microscopy (SEM), the factors that affect the formation of mesophase in C/C composites, such as pressure, quinoline insolubles (QI) and heterocylic compounds, were analyzed. Further, the graphitizability of the resultant carbon was discussed. The results indicate that to some degree, QI contents accelerate the formation of mesophase at atmospheric pressure; while at high pressure, the coalescence and growth of mesophase spherules are impeded and the resultant coke produced from higher QI content pitch is harder to be graphitized. This is in agreement with the transfer of microstructure from domain anisotropy to fine-grained mosaics.

  14. Architectural Visualization of C/C++ Source Code for Program Comprehension

    Energy Technology Data Exchange (ETDEWEB)

    Panas, T; Epperly, T W; Quinlan, D; Saebjornsen, A; Vuduc, R

    2006-09-01

    Structural and behavioral visualization of large-scale legacy systems to aid program comprehension is still a major challenge. The challenge is even greater when applications are implemented in flexible and expressive languages such as C and C++. In this paper, we consider visualization of static and dynamic aspects of large-scale scientific C/C++ applications. For our investigation, we reuse and integrate specialized analysis and visualization tools. Furthermore, we present a novel layout algorithm that permits a compressive architectural view of a large-scale software system. Our layout is unique in that it allows traditional program visualizations, i.e., graph structures, to be seen in relation to the application's file structure.

  15. Diffusion and electrotransport of some transition elements in (B. C. C. ) thorium

    Energy Technology Data Exchange (ETDEWEB)

    Okafor, I.C.I.

    1987-03-01

    Diffusion and electrotransport parameters of the transition elements molybdenum, rhenium, tungsten and zirconium in ..beta.. thorium were measured for the temperature range 1660-1945 K. For each solute element, except zirconium, the measurement was made at four different temperatures, where as for zirconium, studies were performed for only two temperatures 1770 and 1870 K. The authors' results indicate that all four solute elements migrate to the anode in b.c.c. thorium with mean Z/sup */ values of -6.6 for Mo, -4.6 for Re, -8.2 for W and about -2.5 for Zr. The results also indicate that molybdenum, rhenium and tungsten diffuse much faster in ..beta.. thorium than zirconium.

  16. Two Photon Transition Form Factor of $\\bar{c}c $ Quarkonia

    CERN Document Server

    Chen, Jing; Chang, Lei; Liu, Yu-xin

    2016-01-01

    The two photon transition of $\\bar{c}c$ quarkonia are studied within a covariant approach based on the consistent truncation scheme of the quantum chromodynamics Dyson-Schwinger equation for the quark propagator and the Bethe--Salpeter equation for the mesons. We find the decay widths of $\\eta_{c}^{} \\to \\gamma\\gamma$ and $\\chi_{c0,2}^{} \\to \\gamma\\gamma$ in good agreement with experimental data. The obtained transition form factor of $\\eta_{c}^{} \\to \\gamma\\gamma^{\\ast}$ for a wide range of space-like photon momentum transfer squared is also in agreement with the experimental findings of the BABAR experiment. As a by-product, the decay widths of $\\eta_{b}^{},\\chi_{b0,2}^{} \\to \\gamma\\gamma$ and the transition form factor of $\\eta_{b}^{}, \\chi_{c0,b0}^{} \\to\\gamma\\gamma^{\\ast}$ are predicted, which await for experimental test.

  17. The 3D Lima\\c{c}on: Properties and Applications

    CERN Document Server

    Kreismann, Jakob; Sinzinger, Stefan

    2016-01-01

    We perform electromagnetic wave simulations of fully three-dimensional optical Lima\\c{c}on-microcavities, one basis for their future applications in microlasers and photonic devices. The analysis of the three-dimensional modes and far-fields reveals an increase of the quality factors as compared to the two-dimensional case. The structure of the far-field in the third dimension shows pronounced maxima in the emission directionality inclined to the resonator plane which may be exploited for coupling the resonator modes to the environment. This triggers ideas for technical applications, like the suggested sensor that can detect small changes in the environment based on changes in the emission profile.

  18. Iron-Catalyzed C-C Cross-Couplings Using Organometallics.

    Science.gov (United States)

    Guérinot, Amandine; Cossy, Janine

    2016-08-01

    Over the last decades, iron-catalyzed cross-couplings have emerged as an important tool for the formation of C-C bonds. A wide variety of alkenyl, aryl, and alkyl (pseudo)halides have been coupled to organometallic reagents, the most currently used being Grignard reagents. Particular attention has been devoted to the development of iron catalysts for the functionalization of alkyl halides that are generally challenging substrates in classical cross-couplings. The high functional group tolerance of iron-catalyzed cross-couplings has encouraged organic chemists to use them in the synthesis of bioactive compounds. Even if some points remain obscure, numerous studies have been carried out to investigate the mechanism of iron-catalyzed cross-coupling and several hypotheses have been proposed.

  19. Fabrication of SiC-C composite from poycarbosilane, epoxy and polyvinyl butyral resin mixture

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Jin Wook; Park, Dong Won; Jeun, Joon Pyo; Kang, Phil Hyun [Korea Atomic Energy Research Institte, Jeongeup (Korea, Republic of)

    2009-06-15

    Silicon carbide (SiC) has wide application in various industrial fields because of their good high strength and modulus, low density, oxidation resistance and thermal stability. In this study, SiC-C composites were prepared from mixture of polycarbosilane (PCS), epoxy resin, and polyvinyl butyral (PVB) with weight ration of 2/1/1. PCS/epoxy/PVB mixture was cured by electron beam irradiation at 5,000 kGy. The cured composite was pyrolyzed by heat treatment in flowing argon at 1,300 .deg. C for 1 hr. As the result of TGA analysis, the oxidation resistance showed 95.2% residue at 1,500 .deg. C under air.

  20. Influence of substitutional atoms on the Snoek peak of carbon in b.c.c. iron

    Energy Technology Data Exchange (ETDEWEB)

    Saitoh, Hajime; Yoshinaga, Naoki; Ushioda, Kohsaku

    2004-03-08

    The influence of substitutional atoms (Mn, P, Si, Al, Cr, Co) on the C Snoek peak in b.c.c. iron was investigated. In the dilute range of the substitutes, the addition of Co, Mn, Cr, Si, P and Al resulted in the decreases in Snoek peak height in this ascending order. However, the addition of Mn to the Fe-C-P alloy hardly changes Snoek peak height. There is even a case that Snoek peak height is increased by further Mn addition to this alloy. They can be explained systematically by the proposed model wherein the solute carbon present in the influence region where the lattice distortion around the substitute is greater than the threshold value cannot contribute to the Snoek peak. The strain field generated by a substitutional atom due to the difference in atomic size is concluded to be the main reason for the reduction in Snoek peak height.

  1. Microstructure characteristic and formation mechanism of crackfree TaC coating on C/C composite

    Institute of Scientific and Technical Information of China (English)

    LI Guo-dong; XIONG Xiang; HUANG Bai-yun

    2005-01-01

    The microstructure characteristic and formation mechanism of the crackfree and ablation-resistant TaC coating deposited on the C/C composite by Chemical Vapour Deposition(CVD) were investigated, using the reaction system of TaCl5-C3H6-H2-Ar. The results show that the nanosized pore structure formed in the TaC coating interior during CVD process is the main factor to reduce the hardness, elastic modulus, linear expansibility and inner thermal stress. Then crackfree coatings can be prepared and their thermal shock resistance can be enhanced. To obtain the dense and homogeneous matrix surface is necessary for the crackfree and low stress coating. The TaC coating structure that distributes from the dense matrix towards loose coating surface will result in the thick crackfree coating with good thermal shock resistance.

  2. Sintering Behaviour of Al2O3-SiC-C Ramming Mix

    Institute of Scientific and Technical Information of China (English)

    WUXingrong; CAOFeng

    2004-01-01

    Silicon fines, boron acid solid powders and microfine SiO2 as sintering agents were incorporated into Al2O3-SiC-C ramming mix in order to investigated their effects on the microstructure , mechanical properties and sintering behavior of the ramming mix. Results show that all the three agents could improved both densification and mehanical properties markedly, compared to that of non-agent specimens and the effect of the composite of boron acid solid powders and microfine SiO2 is the best. The oxidation resistance increased with the addition of agents, which is supported by densification. Microstructures showed that agent powders could fill pores or produce liquid phases at high temperature, therefore, improve the sintering of the ramming mix.

  3. Sintering Behaviour of Al2O3-SiC-C Ramming Mix

    Institute of Scientific and Technical Information of China (English)

    WU Xingrong; CAO Feng

    2004-01-01

    Silicon fines, boron acid solid powders and microfine SiO2 as sintering agents were incorporated into Al2O3-SiC-C ramming mix in order to investigated their effects on the microstructue,mechanical properties and sintering be-havior of the ramming mix.Results show that all the three agents could improved both densification and mehanical properties markedly,compared to that of non-agent speci-mens and the effect of the composite of boron acid solid powders and microfine SiO2 is the best.The oxidation re-sistance increased with the addition of agents,which is supported by densification.Microstructures shoued that a-gent powders could fill pores or produce liquid phases at high temperatuer,therefore,improve the sintering of the ramming mix.

  4. Overview of C/C-SiC Composite Development for the Orion Launch Abort System

    Science.gov (United States)

    Allen, Lee R.; Valentine, Peter G.; Schofield, Elizabeth S.; Beshears, Ronald D.; Coston, James E.

    2012-01-01

    Past and present efforts by the authors to further understanding of the ceramic matrix composite (CMC) material used in the valve components of the Orion Launch Abort System (LAS) Attitude Control Motor (ACM) will be presented. The LAS is designed to quickly lift the Orion Crew Exploration Vehicle (CEV) away from its launch vehicle in emergency abort scenarios. The ACM is a solid rocket motor which utilizes eight throttleable nozzles to maintain proper orientation of the CEV during abort operations. Launch abort systems have not been available for use by NASA on manned launches since the last Apollo ]Saturn launch in 1975. The CMC material, carbon-carbon/silicon-carbide (C/C-SiC), is manufactured by Fiber Materials, Inc. and consists of a rigid 4-directional carbon-fiber tow weave reinforced with a mixed carbon plus SiC matrix. Several valve and full system (8-valve) static motor tests have been conducted by the motor vendor. The culmination of these tests was the successful flight test of the Orion LAS Pad Abort One (PA ]1) vehicle on May 6, 2010. Due to the fast pace of the LAS development program, NASA Marshall Space Flight Center assisted the LAS community by performing a series of material and component evaluations using fired hardware from valve and full ]system development motor tests, and from the PA-1 flight ACM motor. Information will be presented on the structure of the C/C-SiC material, as well as the efficacy of various non ]destructive evaluation (NDE) techniques, including but not limited to: radiography, computed tomography, nanofocus computed tomography, and X-ray transmission microscopy. Examinations of the microstructure of the material via scanning electron microscopy and energy dispersive spectroscopy will also be discussed. The findings resulting from the subject effort are assisting the LAS Project in risk assessments and in possible modifications to the final ACM operational design.

  5. C,C'-bis(benzodiazaborolyl)dicarba-closo-dodecaboranes: synthesis, structures, photophysics and electrochemistry.

    Science.gov (United States)

    Weber, Lothar; Kahlert, Jan; Brockhinke, Regina; Böhling, Lena; Halama, Johannes; Brockhinke, Andreas; Stammler, Hans-Georg; Neumann, Beate; Nervi, Carlo; Harder, Rachel A; Fox, Mark A

    2013-08-14

    Six new C,C'-bis(benzodiazaborolyl)dicarba-closo-dodecaboranes, 1,A-R2-1,A-C2B10H10, where R represents the group 2-(1,3-Et2-1,3,2-N2BC6H4) or 2-(1,3-Ph2-1,3,2-N2BC6H4) and A is 2, 7 or 12, were synthesized from o-, m-, and p-dicarbadodecaboranes (carboranes) by lithiation and subsequent treatment with the respective 2-bromo-1,3,2-benzodiazaboroles. UV-visible and fluorescence spectra of all carboranes display low energy charge transfer emissions. While such emissions with Stokes shifts between 17,330 and 21,290 cm(-1) are typical for C,C'-bis(aryl)-ortho-carboranes, the observed low-energy emissions with Stokes shifts between 8320 and 15,170 cm(-1) for the meta- and para-isomers are unusual as high-energy emissions are typical for meta- and para-dicarbadodecaboranes. Fluorescence quantum yields (φF) for the novel 1,7- and 1,12-bis(benzodiazaborolyl)-carboranes depend on the substituents at the nitrogen atoms of the heterocycle. Thus, the para-carborane with N-ethyl substituents 1,12-(1',3'-Et2-1',3',2'-N2BC6H4)2-1,12-C2B10H10 has a φF value of 41% in cyclohexane solution and only of 9% in the solid state, whereas the analogous 1,12-(1',3'-Ph2-1',3',2'-N2BC6H4)2-1,12-C2B10H10 shows quantum yields of 3% in cyclohexane solution and 72% in the solid state. X-ray crystallographic, computational and cyclic voltammetry studies for these carboranes are also presented.

  6. The interleukin-4 receptor: signal transduction by a hematopoietin receptor.

    Science.gov (United States)

    Keegan, A D; Pierce, J H

    1994-02-01

    Over the last several years, the receptors for numerous cytokines have been molecularly characterized. Analysis of their amino acid sequences shows that some of these receptors bear certain motifs in their extracellular domains that define a family of receptors called the Hematopoietin receptor superfamily. Significant advances in characterizing the structure, function, and mechanisms of signal transduction have been made for several members of this family. The purpose of this review is to discuss the recent advances made for one of the family members, the interleukin (IL) 4 receptor. Other receptor systems have recently been reviewed elsewhere. The IL-4 receptor consists of, at the minimum, the cloned 140 kDa IL-4-binding chain with the potential for associating with other chains. The IL-4 receptor transduces its signal by activating a tyrosine kinase that phosphorylates cellular substrates, including the receptor itself, and the 170 kDa substrate called 4PS. Phosphorylated 4PS interacts with the SH2 domain of the enzyme PI-3'-kinase and increases its enzymatic activity. These early events in the IL-4 receptor initiated signaling pathway may trigger a series of signals that will ultimately lead to an IL-4 specific biologic outcome.

  7. Direct conversion of cellulose using carbon monoxide and water on a Pt-Mo2C/C catalyst

    KAUST Repository

    Li, Jing

    2014-01-01

    CO and H2O were employed as the hydrogen source for cellulose conversion to polyols. Pt-Mo2C/C tandem catalyst with the Pt-Mo 2C domain responsible for H2 and/or H production and the Pt-C domain for cellulose conversion was fabricated. Considerable polyols were obtained over this tandem Pt-Mo2C/C catalyst. This journal is © 2014 The Royal Society of Chemistry.

  8. Discovering motifs in ranked lists of DNA sequences.

    Directory of Open Access Journals (Sweden)

    Eran Eden

    2007-03-01

    Full Text Available Computational methods for discovery of sequence elements that are enriched in a target set compared with a background set are fundamental in molecular biology research. One example is the discovery of transcription factor binding motifs that are inferred from ChIP-chip (chromatin immuno-precipitation on a microarray measurements. Several major challenges in sequence motif discovery still require consideration: (i the need for a principled approach to partitioning the data into target and background sets; (ii the lack of rigorous models and of an exact p-value for measuring motif enrichment; (iii the need for an appropriate framework for accounting for motif multiplicity; (iv the tendency, in many of the existing methods, to report presumably significant motifs even when applied to randomly generated data. In this paper we present a statistical framework for discovering enriched sequence elements in ranked lists that resolves these four issues. We demonstrate the implementation of this framework in a software application, termed DRIM (discovery of rank imbalanced motifs, which identifies sequence motifs in lists of ranked DNA sequences. We applied DRIM to ChIP-chip and CpG methylation data and obtained the following results. (i Identification of 50 novel putative transcription factor (TF binding sites in yeast ChIP-chip data. The biological function of some of them was further investigated to gain new insights on transcription regulation networks in yeast. For example, our discoveries enable the elucidation of the network of the TF ARO80. Another finding concerns a systematic TF binding enhancement to sequences containing CA repeats. (ii Discovery of novel motifs in human cancer CpG methylation data. Remarkably, most of these motifs are similar to DNA sequence elements bound by the Polycomb complex that promotes histone methylation. Our findings thus support a model in which histone methylation and CpG methylation are mechanistically linked

  9. Binding properties of SUMO-interacting motifs (SIMs) in yeast.

    Science.gov (United States)

    Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

    2015-03-01

    Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

  10. Fitting a mixture model by expectation maximization to discover motifs in biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, T.L.; Elkan, C. [Univ. of California, La Jolla, CA (United States)

    1994-12-31

    The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences. Multiple motifs are found by fitting a mixture model to the data, probabilistically erasing the occurrences of the motif thus found, and repeating the process to find successive motifs. The algorithm requires only a set of unaligned sequences and a number specifying the width of the motifs as input. It returns a model of each motif and a threshold which together can be used as a Bayes-optimal classifier for searching for occurrences of the motif in other databases. The algorithm estimates how many times each motif occurs in each sequence in the dataset and outputs an alignment of the occurrences of the motif. The algorithm is capable of discovering several different motifs with differing numbers of occurrences in a single dataset.

  11. Simulation for F.C.C. deformation texture by modified pencil glide theory[Face Centered Cubic

    Energy Technology Data Exchange (ETDEWEB)

    Masui, H.

    1999-11-26

    Inspired by the pencil glide theory for b.c.c. metal, modified pencil glide theory for f.c.c. metal was proposed, dividing the 12 glide systems of f.c.c. metal into three groups individually composed of eight {l{underscore}brace}111{r{underscore}brace}{l{underscore}angle}110{r{underscore}angle} glide systems around the principal axes X[100], Y[010] and Z[001]. These assumptions yielded two mathematical solutions {Omega}(3) and {Omega}(1). In {Omega}(3), from the three groups with four complete conjugated glide systems composed of, respectively, two glide systems of common {l{underscore}angle}110{r{underscore}angle} direction, only one group with the maximum plastic work may operate if the requirements are satisfied, otherwise glide systems in {Omega}(1) where one of the four conjugated glide systems is zero are activated. The model considering the 12 glide systems of f.c.c. as a whole explained many experimentally stable orientations in axisymmetric and rolling deformation. The differences between the two pencil glide theories for b.c.c. and f.c.c. are also discussed with data.

  12. Pierced Lasso Bundles are a new class of knot-like motifs.

    Directory of Open Access Journals (Sweden)

    Ellinor Haglund

    2014-06-01

    Full Text Available A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements. Recently, we discovered a new structural complexity within this motif created by a disulphide bridge in the long-chain helical bundle cytokine leptin. When oxidized, leptin contains a disulphide bridge creating a covalent-loop through which part of the polypeptide chain is threaded (as seen in knotted proteins. We explored whether other proteins contain a similar intriguing knot-like structure as in leptin and discovered 11 structurally homologous proteins in the PDB. We call this new helical family class the Pierced Lasso Bundle (PLB and the knot-like threaded structural motif a Pierced Lasso (PL. In the current study, we use structure-based simulation to investigate the threading/folding mechanisms for all the PLBs along with three unthreaded homologs as the covalent loop (or lasso in leptin is important in folding dynamics and activity. We find that the presence of a small covalent loop leads to a mechanism where structural elements slipknot to thread through the covalent loop. Larger loops use a piercing mechanism where the free terminal plugs through the covalent loop. Remarkably, the position of the loop as well as its size influences the native state dynamics, which can impact receptor binding and biological activity. This previously unrecognized complexity of knot-like proteins within the helical bundle family comprises a completely new class within the knot family, and the hidden complexity we unraveled in the PLBs is expected to be found in other protein structures outside the four-helix bundles. The insights gained here provide critical new elements for future investigation of this emerging class of proteins, where function and the energetic landscape can be controlled by hidden topology, and should be take into account in ab initio predictions of newly identified protein targets.

  13. Motifs in Triadic Random Graphs based on Steiner Triple Systems

    CERN Document Server

    Winkler, Marco

    2013-01-01

    Conventionally, pairwise relationships between nodes are considered to be the fundamental building blocks of complex networks. However, over the last decade the overabundance of certain sub-network patterns, so called motifs, has attracted high attention. It has been hypothesized, these motifs, instead of links, serve as the building blocks of network structures. Although the relation between a network's topology and the general properties of the system, such as its function, its robustness against perturbations, or its efficiency in spreading information is the central theme of network science, there is still a lack of sound generative models needed for testing the functional role of subgraph motifs. Our work aims to overcome this limitation. We employ the framework of exponential random graphs (ERGMs) to define novel models based on triadic substructures. The fact that only a small portion of triads can actually be set independently poses a challenge for the formulation of such models. To overcome this obst...

  14. Network Motifs in Object-Oriented Software Systems

    CERN Document Server

    Ma, Yutao; Liu, Jing

    2008-01-01

    Nowadays, software has become a complex piece of work that may be beyond our control. Understanding how software evolves over time plays an important role in controlling software development processes. Recently, a few researchers found the quantitative evidence of structural duplication in software systems or web applications, which is similar to the evolutionary trend found in biological systems. To investigate the principles or rules of software evolution, we introduce the relevant theories and methods of complex networks into structural evolution and change of software systems. According to the results of our experiment on network motifs, we find that the stability of a motif shows positive correlation with its abundance and a motif with high Z score tends to have stable structure. These findings imply that the evolution of software systems is based on functional cloning as well as structural duplication and tends to be structurally stable. So, the work presented in this paper will be useful for the analys...

  15. How pathogens use linear motifs to perturb host cell networks

    KAUST Repository

    Via, Allegra

    2015-01-01

    Molecular mimicry is one of the powerful stratagems that pathogens employ to colonise their hosts and take advantage of host cell functions to guarantee their replication and dissemination. In particular, several viruses have evolved the ability to interact with host cell components through protein short linear motifs (SLiMs) that mimic host SLiMs, thus facilitating their internalisation and the manipulation of a wide range of cellular networks. Here we present convincing evidence from the literature that motif mimicry also represents an effective, widespread hijacking strategy in prokaryotic and eukaryotic parasites. Further insights into host motif mimicry would be of great help in the elucidation of the molecular mechanisms behind host cell invasion and the development of anti-infective therapeutic strategies.

  16. Mining Natural-Products Screening Data for Target-Class Chemical Motifs.

    Science.gov (United States)

    Coma, Isabel; Bandyopadhyay, Deepak; Diez, Emilio; Ruiz, Emilio Alvarez; de los Frailes, Maria Teresa; Colmenarejo, Gonzalo

    2014-06-01

    In this article, we describe two complementary data-mining approaches used to characterize the GlaxoSmithKline (GSK) natural-products set (NPS) based on information from the high-throughput screening (HTS) databases. Both methods rely on the aggregation and analysis of a large set of single-shot screening data for a number of biological assays, with the goal to reveal natural-product chemical motifs. One of them is an established method based on the data-driven clustering of compounds using a wide range of descriptors,(1)whereas the other method partitions and hierarchically clusters the data to identify chemical cores.(2,3)Both methods successfully find structural scaffolds that significantly hit different groups of discrete drug targets, compared with their relative frequency of demonstrating inhibitory activity in a large number of screens. We describe how these methods can be applied to unveil hidden information in large single-shot HTS data sets. Applied prospectively, this type of information could contribute to the design of new chemical templates for drug-target classes and guide synthetic efforts for lead optimization of tractable hits that are based on natural-product chemical motifs. Relevant findings for 7TM receptors (7TMRs), ion channels, class-7 transferases (protein kinases), hydrolases, and oxidoreductases will be discussed.

  17. Neurotrophic tyrosine kinase receptor 1 is a direct transcriptional and epigenetic target of IL-13 involved in allergic inflammation.

    Science.gov (United States)

    Rochman, M; Kartashov, A V; Caldwell, J M; Collins, M H; Stucke, E M; Kc, K; Sherrill, J D; Herren, J; Barski, A; Rothenberg, M E

    2015-07-01

    Although interleukin (IL)-13 and neurotrophins are functionally important for the pathogenesis of immune responses, the interaction of these pathways has not been explored. Herein, by interrogating IL-13-induced responses in human epithelial cells we show that neurotrophic tyrosine kinase receptor, type 1 (NTRK1), a cognate, high-affinity receptor for nerve growth factor (NGF), is an early transcriptional IL-13 target. Induction of NTRK1 was accompanied by accumulation of activating epigenetic marks in the promoter; transcriptional and epigenetic changes were signal transducer and activator of transcription 6 dependent. Using eosinophilic esophagitis as a model for human allergic inflammation, we found that NTRK1 was increased in inflamed tissue and dynamically expressed as a function of disease activity and that the downstream mediator of NTRK1 signaling early growth response 1 protein was elevated in allergic inflammatory tissue compared with control tissue. Unlike NTRK1, its ligand NGF was constitutively expressed in control and disease states, indicating that IL-13-stimulated NTRK1 induction is a limiting factor in pathway activation. In epithelial cells, NGF and IL-13 synergistically induced several target genes, including chemokine (C-C motif) ligand 26 (eotaxin-3). In summary, we have demonstrated that IL-13 confers epithelial cell responsiveness to NGF by regulating NTRK1 levels by a transcriptional and epigenetic mechanism and that this process likely contributes to allergic inflammation.

  18. Selection against spurious promoter motifs correlates withtranslational efficiency across bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Froula, Jeffrey L.; Francino, M. Pilar

    2007-05-01

    Because binding of RNAP to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of DNA motifs capable of RNAP-binding across the genome. Here we analyze the distribution of the -10 promoter motifs that bind the {sigma}{sup 70} subunit of RNAP in 42 bacterial genomes. We show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory sequences while eliminating them from the nonfunctional and, in most cases, from the protein coding regions. In some genomes, however, -10 sites are over-represented in the coding sequences; these sites could induce pauses effecting regulatory roles throughout the length of a transcriptional unit. For nonfunctional sequences, the extent of motif under-representation varies across genomes in a manner that broadly correlates with the number of tRNA genes, a good indicator of translational speed and growth rate. This suggests that minimizing the time invested in gene transcription is an important selective pressure against spurious binding. However, selection against spurious binding is detectable in the reduced genomes of host-restricted bacteria that grow at slow rates, indicating that components of efficiency other than speed may also be important. Minimizing the number of RNAP molecules per cell required for transcription, and the corresponding energetic expense, may be most relevant in slow growers. These results indicate that genome-level properties affecting the efficiency of transcription and translation can respond in an integrated manner to optimize gene expression. The detection of selection against promoter motifs in nonfunctional regions also implies that no sequence may evolve free of selective constraints, at least in the relatively small and unstructured genomes of bacteria.

  19. [Specific motifs in the genomes of the family Chlamydiaceae].

    Science.gov (United States)

    Demkin, V V; Kirillova, N V

    2012-01-01

    Specific motifs in the genomes of the family Chlamydiaceae were discussed. The search for genetic markers ofbacteria identification and typing is an urgent problem. The progress in sequencing technology resulted in compilation of the database of genomic nucleotide sequences of bacteria. This raised the problem of the search and selection of genetic targets for identification and typing in bacterial genes based on comparative analysis of complete genomic sequences. The goal of this work was to implement comparative genetic analysis of different species of the family Chlamydiaceae. This analysis was focused to detection of specific motifs capable of serving as genetic marker of this family. The consensus domains were detected using the Visual Basic for Application software for MS Excel. Complete coincidence of segments 25 nucleotide long was used as the test for consensus domain selection. One complete genomic sequence for each of 8 bacterial species was taken for the experiment. The experimental sample did not contain complete sequence of C. suis, because at the moment of this research this species was absence in the database GenBank. Comparative assay of the sequences of the C. trachomatis and other representatives of the family Chlamydiaceae revealed 41 common motifs for 8 Chlamydiaceae species tested in this work. The maximal number of consensus motifs was observed in genes of ribosomal RNA and t-RNA. In addition to genes of r-RNA and t-RNA consensus motifs were observed in 5 genes and 6 intergene segments. The gene CTL0299, CTLO800, dagA, and hctA consensus motifs detected in this work can be regarded as identification domains of the family Chlamydiaceae.

  20. Some results on more flexible versions of Graph Motif

    CERN Document Server

    Rizzi, Romeo

    2012-01-01

    The problems studied in this paper originate from Graph Motif, a problem introduced in 2006 in the context of biological networks. Informally speaking, it consists in deciding if a multiset of colors occurs in a connected subgraph of a vertex-colored graph. Due to the high rate of noise in the biological data, more flexible definitions of the problem have been outlined. We present in this paper two inapproximability results for two different optimization variants of Graph Motif. We also study another definition of the problem, when the connectivity constraint is replaced by modularity. While the problem stays NP-complete, it allows algorithms in FPT for biologically relevant parameterizations.

  1. BayesMD: flexible biological modeling for motif discovery

    DEFF Research Database (Denmark)

    Tang, Man-Hung Eric; Krogh, Anders; Winther, Ole

    2008-01-01

    We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained on trans......We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained...

  2. Migrating C/C++ Software to Mobile Platforms in the ADM Context

    Directory of Open Access Journals (Sweden)

    Liliana Martinez

    2017-03-01

    Full Text Available Software technology is constantly evolving and therefore the development of applications requires adapting software components and applications in order to be aligned to new paradigms such as Pervasive Computing, Cloud Computing and Internet of Things. In particular, many desktop software components need to be migrated to mobile technologies. This migration faces many challenges due to the proliferation of different mobile platforms. Developers usually make applications tailored for each type of device expending time and effort. As a result, new programming languages are emerging to integrate the native behaviors of the different platforms targeted in development projects. In this direction, the Haxe language allows writing mobile applications that target all major mobile platforms. Novel technical frameworks for information integration and tool interoperability such as Architecture-Driven Modernization (ADM proposed by the Object Management Group (OMG can help to manage a huge diversity of mobile technologies. The Architecture-Driven Modernization Task Force (ADMTF was formed to create specifications and promote industry consensus on the modernization of existing applications. In this work, we propose a migration process from C/C++ software to different mobile platforms that integrates ADM standards with Haxe. We exemplify the different steps of the process with a simple case study, the migration of “the Set of Mandelbrot” C++ application. The proposal was validated in Eclipse Modeling Framework considering that some of its tools and run-time environments are aligned with ADM standards.

  3. Effect of infiltrating Si on friction properties of C/C composites

    Institute of Scientific and Technical Information of China (English)

    马运柱; 黄伯云; 熊翔; 肖鹏; 李江鸿; 黄启忠; 易茂忠

    2003-01-01

    In order to improve the friction-wear properties of the C/C composites for aircraft brake pairs, the fric-tion behavior of samples with infiltrating Si was investigated. The influence of Si smearing thickness on frictionproperties was studied in detail. The results show that with the increase of Si smearing thickness and β-SiC content,the friction coefficient reduces from 0.40 to 0.30; the linear wear of stators increases from 2.0 μm to 18.9 μm percycle, and that of rotors increases from 1.4 μm to 22.6 μm per cycle; mass wear of stators increases from 20.6 mgto 126.9 mg per cycle, and that of rotors increases from 13.7 mg to 166.2 mg per cycle. On the other hand, whena large number of inhomogeneous β-SiC particulates are performed, friction surfaces of the samples flake off layer bylayer and many nicks are observed.

  4. Anti-oxidation mechanism of SiC-B4C-C composites

    Institute of Scientific and Technical Information of China (English)

    LIU Qi-cheng; XU Xie-wen; HUANG Qi-zhong; HUANG Bai-yun

    2005-01-01

    Mixture of green petroleum coke, B4C and SiC together with short carbon fiber were employed as starting materials, the mixture was press-formed without any binder after grinding, dense and homogeneous binderless SiC-B4C-C(carbon/ceramic) composites were then obtained after sintering. Composites thus prepared possess excellent anti-oxidation property, that is, mass loss less than 1% within the temperature range from 900 to 1100℃ for 10h. Anti-oxidation mechanism was also discussed from the viewpoint of thermodynamics, excellent anti-oxidation property of materials thus prepared can be discribed to 1) solid SiO2 formed from SiC, which restrains the filtering of oxygen and simultaneously, its volume expansion brought about by the reaction takes roles both walling up the original pores and making the material more compact; 2) liquid B2O3 from the reaction of B4C not only makes the combination with C, B4C and SiC tighter through forming solid solution, but also effect of reaction SiC(s)+2CO(g)=SiO2(s)+3C(s) is an expansive process, which improves the microstructure of the material.

  5. The Infiltration Process and Texture Transition of 2D C/C Composites

    Institute of Scientific and Technical Information of China (English)

    Hejun Li; Guozhong Xu; Kezhi Li; Chuang Wang; Wei Li; Miaoling Li

    2009-01-01

    2D needle-punched fiber felt was infiltrated by a kind of rapid isothermal chemical vapor infiltration technique. The infiltration process and texture transition of the infiltrated C/C composites were investigated. The porosity and the variations of the cumulative pore volume were determined by mercury porosimetry. The texture of matrix carbon was studied under a polarized light microscope. The results show that the relative mass gain of the sample increases directly as the infiltration time at the initial stage until 20 h, and subsequently the increasing rate of the relative mass gain decreases gradually with the prolonging of infiltration time. Three layers of pyrocarbon were formed around fibers. Low-textured pyrocarbon was obtained at the initial stage. With the densification going on, high-textured pyrocarbon was formed on the surface of low-textured pyrocarbon. Then, low-textured pyrocarbon was produced again during the final stage of densification. The texture transition is ascribed to the variation of the ratio of cumulative inner surface area to volume of pores and the gas partial pressure in pores.

  6. The Reovirus Sigmal Aspartic Acid Sandwich: A Trimerization Motif Poised for Conformational Change

    Energy Technology Data Exchange (ETDEWEB)

    Schelling,P.; Guglielml, K.; Kirchner, E.; Paetzold, b.; Dermody, T.; Stehle, T.

    2007-01-01

    Reovirus attachment protein {sigma}1 mediates engagement of receptors on the surface of target cells and undergoes dramatic conformational rearrangements during viral disassembly in the endocytic pathway. The {sigma}1 protein is a filamentous, trimeric molecule with a globular {beta}-barrel head domain. An unusual cluster of aspartic acid residues sandwiched between hydrophobic tyrosines is located at the {sigma}1 subunit interface. A 1.75 {angstrom} structure of the {sigma}1 head domain now reveals two water molecules at the subunit interface that are held strictly in position and interact with neighboring residues. Structural and biochemical analyses of mutants affecting the aspartic acid sandwich indicate that these residues and the corresponding chelated water molecules act as a plug to block the free flow of solvent and stabilize the trimer. This arrangement of residues at the {sigma}1 head trimer interface illustrates a new protein design motif that may confer conformational mobility during cell entry.

  7. The reovirus sigma1 aspartic acid sandwich: a trimerization motif poised for conformational change.

    Science.gov (United States)

    Schelling, Pierre; Guglielmi, Kristen M; Kirchner, Eva; Paetzold, Bernhard; Dermody, Terence S; Stehle, Thilo

    2007-04-13

    Reovirus attachment protein sigma1 mediates engagement of receptors on the surface of target cells and undergoes dramatic conformational rearrangements during viral disassembly in the endocytic pathway. The sigma1 protein is a filamentous, trimeric molecule with a globular beta-barrel head domain. An unusual cluster of aspartic acid residues sandwiched between hydrophobic tyrosines is located at the sigma1 subunit interface. A 1.75-A structure of the sigma1 head domain now reveals two water molecules at the subunit interface that are held strictly in position and interact with neighboring residues. Structural and biochemical analyses of mutants affecting the aspartic acid sandwich indicate that these residues and the corresponding chelated water molecules act as a plug to block the free flow of solvent and stabilize the trimer. This arrangement of residues at the sigma1 head trimer interface illustrates a new protein design motif that may confer conformational mobility during cell entry.

  8. iLIR database: A web resource for LIR motif-containing proteins in eukaryotes

    Science.gov (United States)

    Jacomin, Anne-Claire; Samavedam, Siva; Promponas, Vasilis; Nezis, Ioannis P.

    2016-01-01

    ABSTRACT Atg8-family proteins are the best-studied proteins of the core autophagic machinery. They are essential for the elongation and closure of the phagophore into a proper autophagosome. Moreover, Atg8-family proteins are associated with the phagophore from the initiation of the autophagic process to, or just prior to, the fusion between autophagosomes with lysosomes. In addition to their implication in autophagosome biogenesis, they are crucial for selective autophagy through their ability to interact with selective autophagy receptor proteins necessary for the specific targeting of substrates for autophagic degradation. In the past few years it has been revealed that Atg8-interacting proteins include not only receptors but also components of the core autophagic machinery, proteins associated with vesicles and their transport, and specific proteins that are selectively degraded by autophagy. Atg8-interacting proteins contain a short linear LC3-interacting region/LC3 recognition sequence/Atg8-interacting motif (LIR/LRS/AIM) motif which is responsible for their interaction with Atg8-family proteins. These proteins are referred to as LIR-containing proteins (LIRCPs). So far, many experimental efforts have been carried out to identify new LIRCPs, leading to the characterization of some of them in the past 10 years. Given the need for the identification of LIRCPs in various organisms, we developed the iLIR database (https://ilir.warwick.ac.uk) as a freely available web resource, listing all the putative canonical LIRCPs identified in silico in the proteomes of 8 model organisms using the iLIR server, combined with a Gene Ontology (GO) term analysis. Additionally, a curated text-mining analysis of the literature permitted us to identify novel putative LICRPs in mammals that have not previously been associated with autophagy. PMID:27484196

  9. A Numerical Study on the Thermal Conductivity of 3D Woven C/C Composites at High Temperature

    Science.gov (United States)

    Shigang, Ai; Rujie, He; Yongmao, Pei

    2015-12-01

    Experimental data for Carbon/Carbon (C/C) constituent materials are combined with a three dimensional steady state heat transfer finite element analysis to demonstrate the average in-plane and out-of-plane thermal conductivities (TCs) of C/C composites. The finite element analysis is carried out at two distinct length scales: (a) a micro scale comparable with the diameter of carbon fibres and (b) a meso scale comparable with the carbon fibre yarns. Micro-scale model calculate the TCs at the fibre yarn scale in the three orthogonal directions ( x, y and z). The output results from the micro-scale model are then incorporated in the meso-scale model to obtain the global TCs of the 3D C/C composite. The simulation results are quite consistent with the theoretical and experimental counterparts reported in references. Based on the numerical approach, TCs of the 3D C/C composite are calculated from 300 to 2500 K. Particular attention is given in elucidating the variations of the TCs with temperature. The multi-scale models provide an efficient approach to predict the TCs of 3D textile materials, which is helpful for the thermodynamic property analysis and structure design of the C/C composites.

  10. Amide-directed photoredox-catalysed C-C bond formation at unactivated sp3 C-H bonds

    Science.gov (United States)

    Chu, John C. K.; Rovis, Tomislav

    2016-11-01

    Carbon-carbon (C-C) bond formation is paramount in the synthesis of biologically relevant molecules, modern synthetic materials and commodity chemicals such as fuels and lubricants. Traditionally, the presence of a functional group is required at the site of C-C bond formation. Strategies that allow C-C bond formation at inert carbon-hydrogen (C-H) bonds enable access to molecules that would otherwise be inaccessible and the development of more efficient syntheses of complex molecules. Here we report a method for the formation of C-C bonds by directed cleavage of traditionally non-reactive C-H bonds and their subsequent coupling with readily available alkenes. Our methodology allows for amide-directed selective C-C bond formation at unactivated sp3 C-H bonds in molecules that contain many such bonds that are seemingly indistinguishable. Selectivity arises through a relayed photoredox-catalysed oxidation of a nitrogen-hydrogen bond. We anticipate that our findings will serve as a starting point for functionalization at inert C-H bonds through a strategy involving hydrogen-atom transfer.

  11. Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

    Directory of Open Access Journals (Sweden)

    Farré Domènec

    2007-12-01

    Full Text Available Abstract Background The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes. Results We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters. Conclusion The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.

  12. Nephila clavipes Flagelliform silk-like GGX motifs contribute to extensibility and spacer motifs contribute to strength in synthetic spider silk fibers.

    Science.gov (United States)

    Adrianos, Sherry L; Teulé, Florence; Hinman, Michael B; Jones, Justin A; Weber, Warner S; Yarger, Jeffery L; Lewis, Randolph V

    2013-06-10

    Flagelliform spider silk is the most extensible silk fiber produced by orb weaver spiders, though not as strong as the dragline silk of the spider. The motifs found in the core of the Nephila clavipes flagelliform Flag protein are GGX, spacer, and GPGGX. Flag does not contain the polyalanine motif known to provide the strength of dragline silk. To investigate the source of flagelliform fiber strength, four recombinant proteins were produced containing variations of the three core motifs of the Nephila clavipes flagelliform Flag protein that produces this type of fiber. The as-spun fibers were processed in 80% aqueous isopropanol using a standardized process for all four fiber types, which produced improved mechanical properties. Mechanical testing of the recombinant proteins determined that the GGX motif contributes extensibility and the spacer motif contributes strength to the recombinant fibers. Recombinant protein fibers containing the spacer motif were stronger than the proteins constructed without the spacer that contained only the GGX motif or the combination of the GGX and GPGGX motifs. The mechanical and structural X-ray diffraction analysis of the recombinant fibers provide data that suggests a functional role of the spacer motif that produces tensile strength, though the spacer motif is not clearly defined structurally. These results indicate that the spacer is likely a primary contributor of strength, with the GGX motif supplying mobility to the protein network of native N. clavipes flagelliform silk fibers.

  13. Formación de enlaces C-C, C-N y N-N con catalizadores de óxido de cerio y de oro/óxido de cerio.

    OpenAIRE

    Cómbita Merchán, Diego Fernando

    2016-01-01

    [EN] Heterogeneous catalysis is one of the most important tools in the advancement of green chemistry, understood it as one that efficiently uses (preferably renewable) raw materials, eliminate waste and avoids the use of toxic and/or dangerous reagents and solvents in chemicals production and application. In this thesis we have investigated the reaction mechanisms and the nature of the active centers in C-C, C-N and N-N bond forming reactions over cerium oxide and over gold nanoparticles...

  14. GCC(g++)编译环境下C(C++)和汇编的接口分析%C/C++ Language and Assemble Language Ombination Programming Based on Linux

    Institute of Scientific and Technical Information of China (English)

    郝丽花; 陈付龙

    2004-01-01

    为了在gcc/g++环境下程序开发能顺利地进行C/C++与汇编语言的混合编程,本文给出了一种在该环境下的接口分析方法,并在此基础上分析了gcc/g++环境下汇编源程序如何与调用它的C/C++程序接口问题.

  15. Linear motif atlas for phosphorylation-dependent signaling

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Jensen, LJ; Diella, F;

    2008-01-01

    Systematic and quantitative analysis of protein phosphorylation is revealing dynamic regulatory networks underlying cellular responses to environmental cues. However, matching these sites to the kinases that phosphorylate them and the phosphorylation-dependent binding domains that may subsequently...... sequence models of linear motifs. The atlas is available as a community resource (http://netphorest.info)....

  16. Motifs in triadic random graphs based on Steiner triple systems

    Science.gov (United States)

    Winkler, Marco; Reichardt, Jörg

    2013-08-01

    Conventionally, pairwise relationships between nodes are considered to be the fundamental building blocks of complex networks. However, over the last decade, the overabundance of certain subnetwork patterns, i.e., the so-called motifs, has attracted much attention. It has been hypothesized that these motifs, instead of links, serve as the building blocks of network structures. Although the relation between a network's topology and the general properties of the system, such as its function, its robustness against perturbations, or its efficiency in spreading information, is the central theme of network science, there is still a lack of sound generative models needed for testing the functional role of subgraph motifs. Our work aims to overcome this limitation. We employ the framework of exponential random graph models (ERGMs) to define models based on triadic substructures. The fact that only a small portion of triads can actually be set independently poses a challenge for the formulation of such models. To overcome this obstacle, we use Steiner triple systems (STSs). These are partitions of sets of nodes into pair-disjoint triads, which thus can be specified independently. Combining the concepts of ERGMs and STSs, we suggest generative models capable of generating ensembles of networks with nontrivial triadic Z-score profiles. Further, we discover inevitable correlations between the abundance of triad patterns, which occur solely for statistical reasons and need to be taken into account when discussing the functional implications of motif statistics. Moreover, we calculate the degree distributions of our triadic random graphs analytically.

  17. How curved membranes recruit amphipathic helices and protein anchoring motifs

    DEFF Research Database (Denmark)

    Hatzakis, Nikos; Bhatia, Vikram Kjøller; Larsen, Jannik;

    2009-01-01

    Lipids and several specialized proteins are thought to be able to sense the curvature of membranes (MC). Here we used quantitative fluorescence microscopy to measure curvature-selective binding of amphipathic motifs on single liposomes 50-700 nm in diameter. Our results revealed that sensing...

  18. Observation of Spontaneous C=C Bond Breaking in the Reaction between Atomic Boron and Ethylene in Solid Neon.

    Science.gov (United States)

    Jian, Jiwen; Lin, Hailu; Luo, Mingbiao; Chen, Mohua; Zhou, Mingfei

    2016-07-11

    A ground-state boron atom inserts into the C=C bond of ethylene to spontaneously form the allene-like compound H2 CBCH2 on annealing in solid neon. This compound can further isomerize to the propyne-like HCBCH3 isomer under UV light excitation. The observation of this unique spontaneous C=C bond insertion reaction is consistent with theoretical predictions that the reaction is thermodynamically exothermic and kinetically facile. This work demonstrates that the stronger C=C bond, rather than the less inert C-H bond, can be broken to form organoboron species from the reaction of a boron atom with ethylene even at cryogenic temperatures.

  19. Sequence alignment reveals possible MAPK docking motifs on HIV proteins.

    Directory of Open Access Journals (Sweden)

    Perry Evans

    Full Text Available Over the course of HIV infection, virus replication is facilitated by the phosphorylation of HIV proteins by human ERK1 and ERK2 mitogen-activated protein kinases (MAPKs. MAPKs are known to phosphorylate their substrates by first binding with them at a docking site. Docking site interactions could be viable drug targets because the sequences guiding them are more specific than phosphorylation consensus sites. In this study we use multiple bioinformatics tools to discover candidate MAPK docking site motifs on HIV proteins known to be phosphorylated by MAPKs, and we discuss the possibility of targeting docking sites with drugs. Using sequence alignments of HIV proteins of different subtypes, we show that MAPK docking patterns previously described for human proteins appear on the HIV matrix, Tat, and Vif proteins in a strain dependent manner, but are absent from HIV Rev and appear on all HIV Nef strains. We revise the regular expressions of previously annotated MAPK docking patterns in order to provide a subtype independent motif that annotates all HIV proteins. One revision is based on a documented human variant of one of the substrate docking motifs, and the other reduces the number of required basic amino acids in the standard docking motifs from two to one. The proposed patterns are shown to be consistent with in silico docking between ERK1 and the HIV matrix protein. The motif usage on HIV proteins is sufficiently different from human proteins in amino acid sequence similarity to allow for HIV specific targeting using small-molecule drugs.

  20. An interspecies conserved motif of the mouse immune system-released activating agent (ISRAA) induces proliferative effects on human cells.

    Science.gov (United States)

    Taha, Safa; Fathallah, Mohamed Dahmani; Bakhiet, Moiz

    2014-07-01

    We have recently described an immune system-released activating agent (ISRAA) as a nervous system-induced factor that stimulates immune responses in the mouse spleen. However, the human ISRAA has not yet been identified. In this study, we examined the effects of the mouse ISRAA protein on human peripheral blood mononuclear cells (PBMCs), to observe if the biological activity of this molecule is consistent between the two different species. Mouse ISRAA demonstrated dose-dependent dualistic effects on human cells, as 5 µg exhibited positive apoptosis and 50 pg exhibited significant proliferation (P<0.05). Furthermore, immunosuppressed cells from patients undergoing immunosuppressive therapy demonstrated significant proliferation to 50 pg ISRAA (P<0.05). Studies to compare sequences in different species revealed a preserved motif, exhibiting 72% similarity with the interspecies conserved signal peptide motif of tumor necrosis factor receptor 1 (TNFR1). A mutant ISRAA lacking this motif was produced and tested for its biological effects. The mutant ISRAA demonstrated neither apoptotic nor proliferative effects compared with wild type. Therefore, an interspecies conserved domain of ISRAA constitutes the active site of the molecule, and its effects on immunocompromised cells should be investigated for future therapies in the treatment of immunosuppressive disorders.

  1. Analyzing the activation of the melanocortin-2 receptor of tetrapods.

    Science.gov (United States)

    Dores, Robert M; Liang, Liang

    2014-07-01

    Following the biochemical characterization of the pituitary hormone, adrenocorticotropin (ACTH), in the 1950's, a number of structure/function studies were done which identifies two amino acid motifs in ACTH, the HFRW motif and KKRR motif, as critical for the activation of the "ACTH" receptor on adrenal cortex cells. In the 1990's the "ACTH" receptor was identified as a member of the melanocortin receptor gene family, and given the name melanocortin-2 receptor (MC2R). Since that time a number of studies on both tetrapod and teleost MC2R orthologs have established that these orthologs can only be activated by ACTH, but not by any of the MSH-sized melanocortin ligands, and these orthologs require interaction with the melanocortin-2 receptor accessory protein (MRAP) for functional expression. This review summarizes recent structure/function studies on human ACTH, and points out the importance of the GKPVG motif in ACTH for the activation of the receptor. In this regard, a multiple-step model for the activation of tetrapod and teleost MC2R orthologs is presented, and the evolution of gnathostome MC2R ligand selectivity and the requirement for MRAP interaction is discussed in light of a recent study on a cartilaginous fish MC2R ortholog. This review contains excerpts from the Gorbman/Bern Lecture presented at the Second Meeting of the North American Society for Comparative Endocrinology (NASCE).

  2. Cloning of rat thymic stromal lymphopoietin receptor (TSLPR) and characterization of genomic structure of murine Tslpr gene

    DEFF Research Database (Denmark)

    Blagoev, Blagoy; Nielsen, Mogens M; Angrist, Misha

    2002-01-01

    , a cytokine involved in B- and T-cell function. We have cloned the TSLP receptor from rat and find that the WSXWX motif commonly found in extracellular domains of cytokine receptors is conserved as a W(T/S)XV(T/A) motif among TSLP receptors from mouse, rat and human. As in the mouse, TSLP receptor is widely...... is similar to the expression of several other cytokine receptors that have been characterized thus far. We have also characterized the genomic structure of the murine Tslpr gene which shows that in addition to primary sequence homology, it shares a common genomic organization of coding exons with the murine...

  3. Cloning and expression analysis of human reticulon 4c cDNA

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    RTNs (reticulons) is a gene family related to the growth and differentiation of neuroendocrine cell. This family is composed of several members such as RTN1, RTN2 and RTN3. RTN1 and RTN2 have been proved to have 3 transcripts with different length. Because the RTN1c cDNA was involved in the sologenesis of small cell lung carcinoma (SCLC), it was selected as a bioinformatic probe to clone novel members of RTN family with the electric hybridization assistant new-gene cloning method (EHAC). A 1677-bp cDNA was identified from human brain cDNA library. The cDNA contains an intact open reading frame (ORF) which encodes a protein of 199 amino acids. This deduced protein is highly homologous to RTN1c, RTN2c and RTN3 with identities of 64.4%, 45.8% and 50.0% respectively. This new gene was named RTN4c (GenBank accession number: AF087901). Northern hybridization showed that the full length of RTN4c transcript is about 1.8 kb. It is hardly expressed in heart, placenta, lung, spleen, thymus, testis, ovary, small intestine and peripheral blood white cells; but it is highly expressed in the tissues of skeletal muscle, brain, liver and kidney, and less expressed in the pancreas, prostate and colon. Furthermore, Northern results also showed that there is a 2.3 kb transcript expressed in 14 tissues except liver and skeletal muscle; while another 5.0 kb transcript in brain, skeletal muscle and testis. By the electric hybridization walking, we obtained two full-length contigs with a length of 4632 and 2235 bp respectively. The former encodes a protein with 1192 amino acids and was defined as RTN4a; the latter encodes another protein with 373 amino acids, and was named RTN4b. The RTN4 gene was mapped to human chromosome 2p14-p13 region by the radiation hybridization (RH).

  4. A Bioinformatics Approach for Detecting Repetitive Nested Motifs using Pattern Matching

    Science.gov (United States)

    Romero, José R.; Carballido, Jessica A.; Garbus, Ingrid; Echenique, Viviana C.; Ponzoni, Ignacio

    2016-01-01

    The identification of nested motifs in genomic sequences is a complex computational problem. The detection of these patterns is important to allow the discovery of transposable element (TE) insertions, incomplete reverse transcripts, deletions, and/or mutations. In this study, a de novo strategy for detecting patterns that represent nested motifs was designed based on exhaustive searches for pairs of motifs and combinatorial pattern analysis. These patterns can be grouped into three categories, motifs within other motifs, motifs flanked by other motifs, and motifs of large size. The methodology used in this study, applied to genomic sequences from the plant species Aegilops tauschii and Oryza sativa, revealed that it is possible to identify putative nested TEs by detecting these three types of patterns. The results were validated through BLAST alignments, which revealed the efficacy and usefulness of the new method, which is called Mamushka. PMID:27812277

  5. Computer Simulation of the E.C.C.S. Buckling Curve using a Monte-Carlo Method

    NARCIS (Netherlands)

    Strating, J.; Vos, H.

    1973-01-01

    The application of a Monte-Carlo simulation procedure to obtain the distribution function of the maximum load of a hinged column with imperfections is discussed. Buckling tests carried out by the E.C.C.S. on IPE 160 sections have been simulated. Information concerning the column variables is obtaine

  6. Highly Conductive, Mechanically Robust, and Electrochemically Inactive TiC/C Nanofiber Scaffold for High-Performance Silicon Anode Batteries

    KAUST Repository

    Yao, Yan

    2011-10-25

    Silicon has a high specific capacity of 4200 mAh/g as lithium-ion battery anodes, but its rapid capacity fading due to >300% volume expansion and pulverization presents a significant challenge for practical applications. Here we report a core-shell TiC/C/Si inactive/active nanocomposite for Si anodes demonstrating high specific capacity and excellent electrochemical cycling. The amorphous silicon layer serves as the active material to store Li+, while the inactive TiC/C nanofibers act as a conductive and mechanically robust scaffold for electron transport during the Li-Si alloying process. The core-shell TiC/C/Si nanocomposite anode shows ∼3000 mAh g-1 discharge capacity and 92% capacity retention after 100 charge/discharge cycles. The excellent cycling stability and high rate performance could be attributed to the tapering of the nanofibers and the open structure that allows facile Li ion transport and the high conductivity and mechanical stability of the TiC/C scaffold. © 2011 American Chemical Society.

  7. Synthesis and systematic evaluation of symmetric sulfonated centrally C-C bonded cyanine near-infrared dyes for protein labelling

    NARCIS (Netherlands)

    Wal, Van Der Steffen; Kuil, Joeri; Valentijn, A.R.P.M.; Leeuwen, Van Fijs W.B.

    2016-01-01

    The most commonly used near-infrared cyanine dyes contain an aryl ether that is not fully stable towards nucleophiles. Replacement of the aryl ether by a more stable carbon-carbon bond can improve the stability. In this work we have synthesized a series of four negatively-charged symmetrical C-C

  8. Bite angle effects of diphosphines in C-C and C-X bond forming cross coupling reactions

    NARCIS (Netherlands)

    Birkholz, M.N.; Freixa, Z.; van Leeuwen, P.W.N.M.

    2009-01-01

    Catalytic reactions of C-C and C-X bond formation are discussed in this critical review with particular emphasis on cross coupling reactions catalyzed by palladium and wide bite angle bidentate diphosphine ligands. Especially those studies have been collected that allow comparison of the ligand bite

  9. A mild route to mesoporous Mo2C-C hybrid nanospheres for high performance lithium-ion batteries

    Science.gov (United States)

    Gao, Qing; Zhao, Xinyu; Xiao, Ying; Zhao, Di; Cao, Minhua

    2014-05-01

    In this work, we have developed a mild route to fabricate typically mesoporous Mo2C-C hybrid nanospheres based on a solvothermal synthesis and reduction-carbonization process. This work opens a low-temperature route to synthesize valuable carbides. The resultant Mo2C-C hybrid, for the first time, is used as an anode material in lithium ion batteries (LIBs). Compared with bulk Mo2C, the Mo2C-C hybrid exhibits much better electrochemical performance. Remarkably, the hybrid electrode can deliver a specific capacity of over 670 mA h g-1 after 50 cycles at 100 mA g-1, which is much higher than that of the bulk material (113 mA h g-1). Even cycled at a high current density of 1000 mA g-1, high capacities of around 400-470 mA h g-1 can still be retained for the Mo2C-C hybrid. It might benefit from the synergistic effect of the nanohybridization, effectively relieving the volume change during the repeated lithium insertion-extraction reactions and maintaining the integrity of the electrical connections. It is expected that the present synthesis strategy for the Mo2C-C hybrid can be extended to other nanostructured carbides with good energy storage performance.In this work, we have developed a mild route to fabricate typically mesoporous Mo2C-C hybrid nanospheres based on a solvothermal synthesis and reduction-carbonization process. This work opens a low-temperature route to synthesize valuable carbides. The resultant Mo2C-C hybrid, for the first time, is used as an anode material in lithium ion batteries (LIBs). Compared with bulk Mo2C, the Mo2C-C hybrid exhibits much better electrochemical performance. Remarkably, the hybrid electrode can deliver a specific capacity of over 670 mA h g-1 after 50 cycles at 100 mA g-1, which is much higher than that of the bulk material (113 mA h g-1). Even cycled at a high current density of 1000 mA g-1, high capacities of around 400-470 mA h g-1 can still be retained for the Mo2C-C hybrid. It might benefit from the synergistic effect of

  10. NCBI nr-aa BLAST: CBRC-PCAP-01-1446 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-PCAP-01-1446 ref|NP_001033695.1| chemokine (C-C motif) receptor 1 [Canis lupus... familiaris] dbj|BAE66670.1| chemokine (C-C motif) receptor 1 [Canis lupus familiaris] NP_001033695.1 1e-155 77% ...

  11. A new motif for inhibitors of geranylgeranyl diphosphate synthase.

    Science.gov (United States)

    Foust, Benjamin J; Allen, Cheryl; Holstein, Sarah A; Wiemer, David F

    2016-08-15

    The enzyme geranylgeranyl diphosphate synthase (GGDPS) is believed to receive the substrate farnesyl diphosphate through one lipophilic channel and release the product geranylgeranyl diphosphate through another. Bisphosphonates with two isoprenoid chains positioned on the α-carbon have proven to be effective inhibitors of this enzyme. Now a new motif has been prepared with one isoprenoid chain on the α-carbon, a second included as a phosphonate ester, and the potential for a third at the α-carbon. The pivaloyloxymethyl prodrugs of several compounds based on this motif have been prepared and the resulting compounds have been tested for their ability to disrupt protein geranylgeranylation and induce cytotoxicity in myeloma cells. The initial biological studies reveal activity consistent with GGDPS inhibition, and demonstrate a structure-function relationship which is dependent on the nature of the alkyl group at the α-carbon.

  12. Genetic analysis of beta1 integrin "activation motifs" in mice

    DEFF Research Database (Denmark)

    Czuchra, Aleksandra; Meyer, Hannelore; Legate, Kyle R

    2006-01-01

    tails, leading to tail separation and integrin activation. We analyzed mice in which we mutated the tyrosines of the beta1 tail and the membrane-proximal aspartic acid required for the salt bridge. Tyrosine-to-alanine substitutions abolished beta1 integrin functions and led to a beta1 integrin......-null phenotype in vivo. Surprisingly, neither the substitution of the tyrosines with phenylalanine nor the aspartic acid with alanine resulted in an obvious defect. These data suggest that the NPXY motifs of the beta1 integrin tail are essential for beta1 integrin function, whereas tyrosine phosphorylation......Akey feature of integrins is their ability to regulate the affinity for ligands, a process termed integrin activation. The final step in integrin activation is talin binding to the NPXY motif of the integrin beta cytoplasmic domains. Talin binding disrupts the salt bridge between the alpha/beta...

  13. Endoplasmic reticulum protein targeting of phospholamban: a common role for an N-terminal di-arginine motif in ER retention?

    Directory of Open Access Journals (Sweden)

    Parveen Sharma

    Full Text Available BACKGROUND: Phospholamban (PLN is an effective inhibitor of the sarco(endoplasmic reticulum Ca(2+-ATPase, which transports Ca(2+ into the SR lumen, leading to muscle relaxation. A mutation of PLN in which one of the di-arginine residues at positions 13 and 14 was deleted led to a severe, early onset dilated cardiomyopathy. Here we were interested in determining the cellular mechanisms involved in this disease-causing mutation. METHODOLOGY/PRINCIPAL FINDING: Mutations deleting codons for either or both Arg13 or Arg14 resulted in the mislocalization of PLN from the ER. Our data show that PLN is recycled via the retrograde Golgi to ER membrane traffic pathway involving COP-I vesicles, since co-immunoprecipitation assays determined that COP I interactions are dependent on an intact di-arginine motif as PLN RDelta14 did not co-precipitate with COP I containing vesicles. Bioinformatic analysis determined that the di-arginine motif is present in the first 25 residues in a large number of all ER/SR Gene Ontology (GO annotated proteins. Mutations in the di-arginine motif of the Sigma 1-type opioid receptor, the beta-subunit of the signal recognition particle receptor, and Sterol-O-acyltransferase, three proteins identified in our bioinformatic screen also caused mislocalization of these known ER-resident proteins. CONCLUSION: We conclude that PLN is enriched in the ER due to COP I-mediated transport that is dependent on its intact di-arginine motif and that the N-terminal di-arginine motif may act as a general ER retrieval sequence.

  14. Characterizing regulatory path motifs in integrated networks using perturbational data

    OpenAIRE

    Joshi, Anagha Madhusudan; Van Parys, Thomas; de Peer, Yves Van; Michoel, Tom

    2010-01-01

    We introduce Pathicular http://bioinformatics.psb.ugent.be/software/details/Pathicular, a Cytoscape plugin for studying the cellular response to perturbations of transcription factors by integrating perturbational expression data with transcriptional, protein-protein and phosphorylation networks. Pathicular searches for 'regulatory path motifs', short paths in the integrated physical networks which occur significantly more often than expected between transcription factors and their targets in...

  15. Neoanalysis, Orality, and Intertextuality: An Examination of Homeric Motif Transference

    Directory of Open Access Journals (Sweden)

    Jonathan Burgess

    2006-03-01

    Full Text Available In Homeric studies scholars have speculated on the influence of (non-surviving preHomeric material on the Iliad. This article expands this line of argument from an oralist perspective, with reference to modern intertextual theory. It concludes that preHomeric and nonHomeric motifs from oral traditions were transferred into the epic poem, creating an intertextually allusive poetics that would have been recognizable to an early Greek audience informed of mythological traditions.

  16. A Cooperative Approach for the Extraction of Protein Motifs

    Institute of Scientific and Technical Information of China (English)

    Chao CHEN; Yuan Xin TIAN; Xiao Yong ZOU; Pei Xiang CAI; Jin Yuan MO

    2006-01-01

    By integrating the concept of cooperative approach, an extension of the fast annealing coevolutionary algorithm is presented in this paper. It outperformed the original algorithm in the domain of function optimization, especially in terms of convergence rate. It was also applied to a real optimization problem, protein motif extraction. And a satisfactory result has been obtained with the accuracy of prediction achieving 67.0%, which is in agreement with the result in the PROSITE database.

  17. The leitmotif racket in Lolita—marginal notes on Nabokov’s use of motifs

    OpenAIRE

    2013-01-01

    This is a study of Nabokov’s use of leitmotifs in Lolita, a study of how they intertwine and interact, and the problems Nabokov’s stylistic dexterity pose to the reader and critic. It traces prominent occurrences of the toilet and telephone motifs, and their connection with motifs like the slipper and the racket motif.

  18. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

    LENUS (Irish Health Repository)

    Casey, Fergal

    2011-08-22

    Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

  19. MAR characteristic motifs mediate episomal vector in CHO cells.

    Science.gov (United States)

    Lin, Yan; Li, Zhaoxi; Wang, Tianyun; Wang, Xiaoyin; Wang, Li; Dong, Weihua; Jing, Changqin; Yang, Xianjun

    2015-04-01

    An ideal gene therapy vector should enable persistent transgene expression without limitations in safety and reproducibility. Recent researches' insight into the ability of chromosomal matrix attachment regions (MARs) to mediate episomal maintenance of genetic elements allowed the development of a circular episomal vector. Although a MAR-mediated engineered vector has been developed, little is known on which motifs of MAR confer this function during interaction with the host genome. Here, we report an artificially synthesized DNA fragment containing only characteristic motif sequences that served as an alternative to human beta-interferon matrix attachment region sequence. The potential of the vector to mediate gene transfer in CHO cells was investigated. The short synthetic MAR motifs were found to mediate episomal vector at a low copy number for many generations without integration into the host genome. Higher transgene expression was maintained for at least 4 months. In addition, MAR was maintained episomally and conferred sustained EGFP expression even in nonselective CHO cells. All the results demonstrated that MAR characteristic sequence-based vector can function as stable episomes in CHO cells, supporting long-term and effective transgene expression.

  20. Process-based network decomposition reveals backbone motif structure.

    Science.gov (United States)

    Wang, Guanyu; Du, Chenghang; Chen, Hao; Simha, Rahul; Rong, Yongwu; Xiao, Yi; Zeng, Chen

    2010-06-08

    A central challenge in systems biology today is to understand the network of interactions among biomolecules and, especially, the organizing principles underlying such networks. Recent analysis of known networks has identified small motifs that occur ubiquitously, suggesting that larger networks might be constructed in the manner of electronic circuits by assembling groups of these smaller modules. Using a unique process-based approach to analyzing such networks, we show for two cell-cycle networks that each of these networks contains a giant backbone motif spanning all the network nodes that provides the main functional response. The backbone is in fact the smallest network capable of providing the desired functionality. Furthermore, the remaining edges in the network form smaller motifs whose role is to confer stability properties rather than provide function. The process-based approach used in the above analysis has additional benefits: It is scalable, analytic (resulting in a single analyzable expression that describes the behavior), and computationally efficient (all possible minimal networks for a biological process can be identified and enumerated).

  1. THE MOTIF OF THE PRODIGAL SON IN IVAN TURGENEV'S NOVELS

    Directory of Open Access Journals (Sweden)

    Valentina Ivanovna Gabdullina

    2013-11-01

    Full Text Available The author questions the perception of Ivan Turgenev as a “non- Christian writer” and studies the problem of the prodigal son motif functioning in a series of his novels. In his novels, Turgenev pictured different phases of the archetypal story, originating from the Gospel parable of the prodigal son. In the novel Rudin he depicted the phase of spiritual wanderings of the hero who had lost touch with his native land — Russia. In his next novels (Home of the Gentry, Fathers and Sons and Smoke, after leading his hero in circles and sending him back to his paternal home, Turgenev reconstructs the model of human behavior, represented in the parable, thereby recognizing the immutability of the idea formalized in the Gospel. The motif of the return to Russian land gets its completion in Turgenev's last novel Virgin Soil, in which the author paradoxically connects the Westernist idea with the Gospel imperative. Solomin, the son of a deacon, sent by his wise father out to Europe “to get education”, studies in England, masters the European knowledge and returns back “to his native land” to establish his own business in inland Russia. Thus, a series of Turgenev's novels, in which he portrayed different phases of social life, are interlinked with the motif of the prodigal son, who is represented by novels' main characters.

  2. Motif structure and cooperation in real-world complex networks

    Science.gov (United States)

    Salehi, Mostafa; Rabiee, Hamid R.; Jalili, Mahdi

    2010-12-01

    Networks of dynamical nodes serve as generic models for real-world systems in many branches of science ranging from mathematics to physics, technology, sociology and biology. Collective behavior of agents interacting over complex networks is important in many applications. The cooperation between selfish individuals is one of the most interesting collective phenomena. In this paper we address the interplay between the motifs’ cooperation properties and their abundance in a number of real-world networks including yeast protein-protein interaction, human brain, protein structure, email communication, dolphins’ social interaction, Zachary karate club and Net-science coauthorship networks. First, the amount of cooperativity for all possible undirected subgraphs with three to six nodes is calculated. To this end, the evolutionary dynamics of the Prisoner’s Dilemma game is considered and the cooperativity of each subgraph is calculated as the percentage of cooperating agents at the end of the simulation time. Then, the three- to six-node motifs are extracted for each network. The significance of the abundance of a motif, represented by a Z-value, is obtained by comparing them with some properly randomized versions of the original network. We found that there is always a group of motifs showing a significant inverse correlation between their cooperativity amount and Z-value, i.e. the more the Z-value the less the amount of cooperativity. This suggests that networks composed of well-structured units do not have good cooperativity properties.

  3. Insertion of tetracysteine motifs into dopamine transporter extracellular domains.

    Directory of Open Access Journals (Sweden)

    Deanna M Navaroli

    Full Text Available The neuronal dopamine transporter (DAT is a major determinant of extracellular dopamine (DA levels and is the primary target for a variety of addictive and therapeutic psychoactive drugs. DAT is acutely regulated by protein kinase C (PKC activation and amphetamine exposure, both of which modulate DAT surface expression by endocytic trafficking. In order to use live imaging approaches to study DAT endocytosis, methods are needed to exclusively label the DAT surface pool. The use of membrane impermeant, sulfonated biarsenic dyes holds potential as one such approach, and requires introduction of an extracellular tetracysteine motif (tetraCys; CCPGCC to facilitate dye binding. In the current study, we took advantage of intrinsic proline-glycine (Pro-Gly dipeptides encoded in predicted DAT extracellular domains to introduce tetraCys motifs into DAT extracellular loops 2, 3, and 4. [(3H]DA uptake studies, surface biotinylation and fluorescence microscopy in PC12 cells indicate that tetraCys insertion into the DAT second extracellular loop results in a functional transporter that maintains PKC-mediated downregulation. Introduction of tetraCys into extracellular loops 3 and 4 yielded DATs with severely compromised function that failed to mature and traffic to the cell surface. This is the first demonstration of successful introduction of a tetracysteine motif into a DAT extracellular domain, and may hold promise for use of biarsenic dyes in live DAT imaging studies.

  4. Event Networks and the Identification of Crime Pattern Motifs.

    Directory of Open Access Journals (Sweden)

    Toby Davies

    Full Text Available In this paper we demonstrate the use of network analysis to characterise patterns of clustering in spatio-temporal events. Such clustering is of both theoretical and practical importance in the study of crime, and forms the basis for a number of preventative strategies. However, existing analytical methods show only that clustering is present in data, while offering little insight into the nature of the patterns present. Here, we show how the classification of pairs of events as close in space and time can be used to define a network, thereby generalising previous approaches. The application of graph-theoretic techniques to these networks can then offer significantly deeper insight into the structure of the data than previously possible. In particular, we focus on the identification of network motifs, which have clear interpretation in terms of spatio-temporal behaviour. Statistical analysis is complicated by the nature of the underlying data, and we provide a method by which appropriate randomised graphs can be generated. Two datasets are used as case studies: maritime piracy at the global scale, and residential burglary in an urban area. In both cases, the same significant 3-vertex motif is found; this result suggests that incidents tend to occur not just in pairs, but in fact in larger groups within a restricted spatio-temporal domain. In the 4-vertex case, different motifs are found to be significant in each case, suggesting that this technique is capable of discriminating between clustering patterns at a finer granularity than previously possible.

  5. Signal Inhibitory Receptor on Leukocytes-1 (SIRL-1), a potent regulator of neutrophil function

    OpenAIRE

    Avondt, K.

    2014-01-01

    In this thesis, we aimed to better understand the role of the immune inhibitory receptor Signal Inhibitory Receptor on Leukocytes-1 (SIRL-1) in neutrophil functions. Inhibitory receptors play a crucial role in tailoring immune responses. SIRL-1 belongs to a family of transmembrane receptors, the Ig superfamily, and is mainly expressed on granulocytes and monocytes. SIRL-1 contains two immunoreceptor tyrosine-based inhibitory motifs (ITIMs) in its cytoplasmic domain and recruits the phosphatas...

  6. C/C++代码自动生成脚本语言接口的实现%Implementation of Automatic Generating Scripting Language Interfaces with C/C++ Code

    Institute of Scientific and Technical Information of China (English)

    官尚元; 张芝萍; 徐立锋; 缪敬

    2005-01-01

    对于开发灵活的科学软件来说,脚本语言是一个强大的工具.然而开发人员经常遇到一个问题:如何将编译过的C/C++代码集成到一个解释器.为了解决上述问题,设计了一个可扩展的编译器--接口产生器(IG).IG主要任务是把编译过的C/C++代码集成到脚本语言解释器中.因此,该文的主要目的就是解决上述相关问题.

  7. Molecular determinants of odorant receptor function in insects

    Indian Academy of Sciences (India)

    Anandasankar Ray; Wynand Van Der Goes Van Naters; John R Carlson

    2014-09-01

    The olfactory system of Drosophila melanogaster provides a powerful model to study molecular and cellular mechanisms underlying function of a sensory system. In the 1970s Siddiqi and colleagues pioneered the application of genetics to olfactory research and isolated several mutant Drosophila with odorant-specific defects in olfactory behaviour, suggesting that odorants are detected differentially by the olfactory system. Since then basic principles of olfactory system function and development have emerged using Drosophila as a model. Nearly four decades later we can add computational methods to further our understanding of how specific odorants are detected by receptors. Using a comparative approach we identify two categories of short amino acid sequence motifs: ones that are conserved family-wide predominantly in the C-terminal half of most receptors, and ones that are present in receptors that detect a specific odorant, 4-methylphenol, found predominantly in the N-terminal half. The odorant-specific sequence motifs are predictors of phenol detection in Anopheles gambiae and other insects, suggesting they are likely to participate in odorant binding. Conversely, the family-wide motifs are expected to participate in shared functions across all receptors and a mutation in the most conserved motif leads to a reduction in odor response. These findings lay a foundation for investigating functional domains within odorant receptors that can lead to a molecular understanding of odor detection.

  8. A novel Bayesian DNA motif comparison method for clustering and retrieval.

    Directory of Open Access Journals (Sweden)

    Naomi Habib

    2008-02-01

    Full Text Available Characterizing the DNA-binding specificities of transcription factors is a key problem in computational biology that has been addressed by multiple algorithms. These usually take as input sequences that are putatively bound by the same factor and output one or more DNA motifs. A common practice is to apply several such algorithms simultaneously to improve coverage at the price of redundancy. In interpreting such results, two tasks are crucial: clustering of redundant motifs, and attributing the motifs to transcription factors by retrieval of similar motifs from previously characterized motif libraries. Both tasks inherently involve motif comparison. Here we present a novel method for comparing and merging motifs, based on Bayesian probabilistic principles. This method takes into account both the similarity in positional nucleotide distributions of the two motifs and their dissimilarity to the background distribution. We demonstrate the use of the new comparison method as a basis for motif clustering and retrieval procedures, and compare it to several commonly used alternatives. Our results show that the new method outperforms other available methods in accuracy and sensitivity. We incorporated the resulting motif clustering and retrieval procedures in a large-scale automated pipeline for analyzing DNA motifs. This pipeline integrates the results of various DNA motif discovery algorithms and automatically merges redundant motifs from multiple training sets into a coherent annotated library of motifs. Application of this pipeline to recent genome-wide transcription factor location data in S. cerevisiae successfully identified DNA motifs in a manner that is as good as semi-automated analysis reported in the literature. Moreover, we show how this analysis elucidates the mechanisms of condition-specific preferences of transcription factors.

  9. Statically Detecting Likely Buffer Overflow Vulnerabilities in C/C++ Program%C/C++源程序缓冲区溢出漏洞的静态检测

    Institute of Scientific and Technical Information of China (English)

    杨小龙; 刘坚

    2004-01-01

    讨论了C/C++源程序中缓冲区溢出的常见表现;分析了其特性以及产生机理;提出了在源代码的AST上附加安全属性进行漏洞静态检测的方法;讨论了该方法的实现过程.

  10. Deep Analysis and Application of the Function Pointer in the C/C++ Language Programming%C/C++语言中函数指针的深入分析与应用

    Institute of Scientific and Technical Information of China (English)

    张海平

    2009-01-01

    C/C++语言程序设计中函数指针进行了详细的分析与研究,包括函数指针的概念、定义和调用,并着重通过回调函数与简单消息映射实例阐述函数指针的使用方法和技巧.

  11. Ubiquitous transgenic overexpression of C-C chemokine ligand 2: a model to assess the combined effect of high energy intake and continuous low-grade inflammation.

    Science.gov (United States)

    Rodríguez-Gallego, Esther; Riera-Borrull, Marta; Hernández-Aguilera, Anna; Mariné-Casadó, Roger; Rull, Anna; Beltrán-Debón, Raúl; Luciano-Mateo, Fedra; Menendez, Javier A; Vazquez-Martin, Alejandro; Sirvent, Juan J; Martín-Paredero, Vicente; Corbí, Angel L; Sierra-Filardi, Elena; Aragonès, Gerard; García-Heredia, Anabel; Camps, Jordi; Alonso-Villaverde, Carlos; Joven, Jorge

    2013-01-01

    Excessive energy management leads to low-grade, chronic inflammation, which is a significant factor predicting noncommunicable diseases. In turn, inflammation, oxidation, and metabolism are associated with the course of these diseases; mitochondrial dysfunction seems to be at the crossroads of mutual relationships. The migration of immune cells during inflammation is governed by the interaction between chemokines and chemokine receptors. Chemokines, especially C-C-chemokine ligand 2 (CCL2), have a variety of additional functions that are involved in the maintenance of normal metabolism. It is our hypothesis that a ubiquitous and continuous secretion of CCL2 may represent an animal model of low-grade chronic inflammation that, in the presence of an energy surplus, could help to ascertain the afore-mentioned relationships and/or to search for specific therapeutic approaches. Here, we present preliminary data on a mouse model created by using targeted gene knock-in technology to integrate an additional copy of the CCl2 gene in the Gt(ROSA)26Sor locus of the mouse genome via homologous recombination in embryonic stem cells. Short-term dietary manipulations were assessed and the findings include metabolic disturbances, premature death, and the manipulation of macrophage plasticity and autophagy. These results raise a number of mechanistic questions for future study.

  12. Ubiquitous Transgenic Overexpression of C-C Chemokine Ligand 2: A Model to Assess the Combined Effect of High Energy Intake and Continuous Low-Grade Inflammation

    Directory of Open Access Journals (Sweden)

    Esther Rodríguez-Gallego

    2013-01-01

    Full Text Available Excessive energy management leads to low-grade, chronic inflammation, which is a significant factor predicting noncommunicable diseases. In turn, inflammation, oxidation, and metabolism are associated with the course of these diseases; mitochondrial dysfunction seems to be at the crossroads of mutual relationships. The migration of immune cells during inflammation is governed by the interaction between chemokines and chemokine receptors. Chemokines, especially C-C-chemokine ligand 2 (CCL2, have a variety of additional functions that are involved in the maintenance of normal metabolism. It is our hypothesis that a ubiquitous and continuous secretion of CCL2 may represent an animal model of low-grade chronic inflammation that, in the presence of an energy surplus, could help to ascertain the afore-mentioned relationships and/or to search for specific therapeutic approaches. Here, we present preliminary data on a mouse model created by using targeted gene knock-in technology to integrate an additional copy of the CCl2 gene in the Gt(ROSA26Sor locus of the mouse genome via homologous recombination in embryonic stem cells. Short-term dietary manipulations were assessed and the findings include metabolic disturbances, premature death, and the manipulation of macrophage plasticity and autophagy. These results raise a number of mechanistic questions for future study.

  13. Leucine zipper motif in RRS1 is crucial for the regulation of Arabidopsis dual resistance protein complex RPS4/RRS1.

    Science.gov (United States)

    Narusaka, Mari; Toyoda, Kazuhiro; Shiraishi, Tomonori; Iuchi, Satoshi; Takano, Yoshitaka; Shirasu, Ken; Narusaka, Yoshihiro

    2016-01-11

    Arabidopsis thaliana leucine-rich repeat-containing (NLR) proteins RPS4 and RRS1, known as dual resistance proteins, confer resistance to multiple pathogen isolates, such as the bacterial pathogens Pseudomonas syringae and Ralstonia solanacearum and the fungal pathogen Colletotrichum higginsianum. RPS4 is a typical Toll/interleukin 1 Receptor (TIR)-type NLR, whereas RRS1 is an atypical TIR-NLR that contains a leucine zipper (LZ) motif and a C-terminal WRKY domain. RPS4 and RRS1 are localised near each other in a head-to-head orientation. In this study, direct mutagenesis of the C-terminal LZ motif in RRS1 caused an autoimmune response and stunting in the mutant. Co-immunoprecipitation analysis indicated that full-length RPS4 and RRS1 are physically associated with one another. Furthermore, virus-induced gene silencing experiments showed that hypersensitive-like cell death triggered by RPS4/LZ motif-mutated RRS1 depends on EDS1. In conclusion, we suggest that the RRS1-LZ motif is crucial for the regulation of the RPS4/RRS1 complex.

  14. 将Python嵌入到C/C++应用程序中的编程方法

    Institute of Scientific and Technical Information of China (English)

    何炯

    2002-01-01

    Python是一种面向对象的语言.本文介绍了怎样在不同的层次上将Python编译器作为一种扩展语言嵌入到用C/C++编写的应用程序之中.嵌入了Python的C/C++应用程序可以完成某些Python特有的功能.文章也讲述了如何扩展嵌入的Python使其获得应用程序本身的功能.最后,讲述了怎样使链接到静态库的应用程序获得动态扩展.

  15. Predicting the Dielectric Strength of c-C4F8 and SF6 Gas Mixtures by Monte Carlo Method

    Institute of Scientific and Technical Information of China (English)

    WU Bian-tao; XIAO Deng-ming

    2007-01-01

    An improved Monte Carlo method was used to simulate the motion of electrons in c-C4F8 and SF6 gas mixtures for pulsed townsend discharge. The electron swarm parameters such as effective ionization coefficient, (-α) and drift velocity over the E/N range from 280~700 Td(1Td= 10-21 V·m2) were calculated by employing a set of cross sections available in literature. From the variation cure of (-α) with SF6 partial pressure p, the limiting field (E/N)lim of gas mixture at different gas content was determined. It is found that the limiting field of c-C4F8 and SF6gas mixture is higher than that of pure SF6 at any SF6 mixture ratio. Simulation results show excellent agreement with experiment data available in previous literature.

  16. Application of Sol Self-Clean Bonded Al2O3-SiC-C Castable for Iron Runner

    Institute of Scientific and Technical Information of China (English)

    XU Guotao; ZHANG Honglei; CHEN Huasheng; WANG Yue; LI Huaiyuan; XIONG Yafei

    2006-01-01

    The properties and microstructure of sol self-clean bonded Al2O3-SiC-C castable in iron runner were studied, and the relation between the amount of sol selfclean binder and the properties of castable were discussed. It is believed that the addition of sol self-clean binder can improve the compressive strength, but has little effect on the bulk density and the apparent porosity,which enable the castable to be applicable in different conditions.

  17. Spheroidization behavior of dendritic b.c.c. phase in Zr-based モ-phase composite

    Directory of Open Access Journals (Sweden)

    Sun Guoyuan

    2013-03-01

    Full Text Available The spheroidization behavior of the dendritic b.c.c. phase dispersed in a bulk metallic glass (BMG matrix was investigated through applying semi-solid isothermal processing and a subsequent rapid quenching procedure to a Zr-based モ-phase composite. The Zr-based composite with the composition of Zr56.2Ti13.8Nb5.0Cu6.9Ni5.6Be12.5 was prefabricated by a water-cooled copper mold-casting method and characterized by X-ray diffraction (XRD and scanning electron microscope (SEM. The results show that the composite consists of a glassy matrix and uniformly distributed fine dendrites of the モ-Zr solid solution with the body-centered-cubic (b.c.c. structure. Based on the differential scanning calorimeter (DSC examination results, and in view of the b.c.c. モ-Zr to h.c.p. メ-Zr phase transition temperature, a semi-solid holding temperature of 900 ìC was determined. After reheating the prefabricated composite to the semi-solid temperature, followed by an isothermal holding process at this temperature for 5 min, and then quenching the semi-solid mixture into iced-water; the two-phase microstructure composed of a BMG matrix and uniformly dispersed spherical b.c.c. モ-Zr particles with a high degree of sphericity was achieved. The present spheroidization transition is a thermodynamically autonomic behavior, and essentially a diffusion process controlled by kinetic factors; and the formation of the BMG matrix should be attributed to the rapid quenching of the semi-solid mixture as well as the large glass-forming ability of the remaining melt in the semi-solid mixture.

  18. 76 FR 39254 - Airworthiness Directives; Schweizer Aircraft Corporation (Schweizer) Model 269A, A-1, B, C, C-1...

    Science.gov (United States)

    2011-07-06

    ... Corporation (Schweizer) Model 269A, A-1, B, C, C-1, and TH-55 Series Helicopters AGENCY: Federal Aviation... reviewed Schweizer Service Bulletins No. B-295 for Model 269A, A-1, B, and C helicopters, and No. C1B-032... continues to read as follows: Authority: 49 U.S.C. 106(g), 40113, 44701. Sec. 39.13 0 2. The FAA amends...

  19. Search for the weak decays J/psi -> D-s(()*()-) e(+)nu(e) + c.c.

    NARCIS (Netherlands)

    Ablikim, M.; Achasov, M. N.; Ai, X. C.; Albayrak, O.; Albrecht, M.; Ambrose, D. J.; Amoroso, A.; An, F. F.; An, Q.; Bai, J. Z.; Ferroli, R. Baldini; Ban, Y.; Bennett, D. W.; Bennett, J. V.; Bertani, M.; Bettoni, D.; Bian, J. M.; Bianchi, F.; Boger, E.; Bondarenko, O.; Boyko, I.; Briere, R. A.; Cai, H.; Cai, X.; Cakir, O.; Calcaterra, A.; Cao, G. F.; Cetin, S. A.; Chang, J. F.; Chelkov, G.; Chen, G.; Chen, H. S.; Chen, H. Y.; Chen, J. C.; Chen, M. L.; Chen, S. J.; Chen, X.; Chen, X. R.; Chen, Y. B.; Cheng, H. P.; Chu, X. K.; Chu, Y. P.; Cibinetto, G.; Cronin-Hennessy, D.; Dai, H. L.; Dai, J. P.; Dedovich, D.; Deng, Z. Y.; Denig, A.; Denysenko, I.; Destefanis, M.; De Mori, F.; Ding, Y.; Dong, C.; Dong, J.; Dong, L. Y.; Dong, M. Y.; Du, S. X.; Duan, P. F.; Fan, J. Z.; Fang, J.; Fang, S. S.; Fang, X.; Fang, Y.; Fava, L.; Feldbauer, F.; Felici, G.; Feng, C. Q.; Fioravanti, E.; Fu, C. D.; Gao, Q.; Gao, Y.; Garzia, I.; Goetzen, K.; Gong, W. X.; Gradl, W.; Greco, M.; Gu, M. H.; Gu, Y. T.; Guan, Y. H.; Guo, A. Q.; Guo, L. B.; Guo, T.; Guo, Y.; Guo, Y. P.; Haddadi, Z.; Hafner, A.; Han, S; Han, Y. L.; Harris, F. A.; He, K. L.; He, Z. Y.; Held, T.; Heng, Y. K.; Hou, Z. L.; Hu, C.; Hu, H. M.; Hu, J. F.; Hu, T.; Hu, Y.; Huang, G. M.; Huang, G. S.; Huang, H. P.; Huang, J. S.; Huang, X. T.; Huang, Y.; Hussain, T.; Ji, Q.; Ji, Q. P.; Ji, X. B.; Ji, X. L.; Jiang, L. L.; Jiang, L. W.; Jiang, X. S.; Jiao, J. B.; Jiao, Z.; Jin, D. P.; Jin, S.; Johansson, T.; Julin, A.; Kalantar-Nayestanaki, N.; Kang, X. L.; Kang, X. S.; Kavatsyuk, M.; Ke, B. C.; Kliemt, R.; Kloss, B.; Kolcu, O. B.; Kopf, B.; Kornicer, M.; Kuehn, W.; Kupsc, A.; Lai, W.; Lange, J. S.; Lara, M.; Larin, P.; Li, C. H.; Li, Cheng; Li, D. M.; Li, F.; Li, G.; Li, H. B.; Li, J. C.; Li, Jin; Li, K.; Li, K.; Li, P. R.; Li, T.; Li, W. D.; Li, W. G.; Li, X. L.; Li, X. M.; Li, X. N.; Li, X. Q.; Li, Z. B.; Liang, H.; Liang, Y. F.; Liang, Y. T.; Liao, G. R.; Lin, D. X.; Liu, B. J.; Liu, C. L.; Liu, C. X.; Liu, F. H.; Liu, Fang; Liu, Feng; Liu, H. B.; Liu, H. H.; Liu, H. H.; Liu, H. M.; Liu, J.; Liu, J. P.; Liu, J. Y.; Liu, K.; Liu, K. Y.; Liu, L. D.; Liu, Q.; Liu, S. B.; Liu, X.; Liu, X. X.; Liu, Y. B.; Liu, Z. A.; Liu, Zhiqiang; Liu, Zhiqing; Loehner, H.; Lou, X. C.; Lu, H. J.; Lu, J. G.; Lu, R. Q.; Lu, Y.; Lu, Y. P.; Luo, C. L.; Luo, M. X.; Luo, T.; Luo, X. L.; Lv, M.; Lyu, X. R.; Ma, F. C.; Ma, H. L.; Ma, L. L.; Ma, Q. M.; Ma, S.; Ma, T.; Ma, X. N.; Ma, X. Y.; Maas, F. E.; Maggiora, M.; Malik, Q. A.; Mao, Y. J.; Mao, Z. P.; Marcello, S.; Messchendorp, J. G.; Min, J.; Min, T. J.; Mitchell, R. E.; Mo, X. H.; Mo, Y. J.; Moeini, H.; Morales, C. Morales; Moriya, K.; Muchnoi, N. Yu.; Muramatsu, H.; Nefedov, Y.; Nerling, F.; Nikolaev, I. B.; Ning, Z.; Nisar, S.; Niu, S. L.; Niu, X. Y.; Olsen, S. L.; Ouyang, Q.; Pacetti, S.; Patteri, P.; Pelizaeus, M.; Peng, H. P.; Peters, K.; Ping, J. L.; Ping, R. G.; Poling, R.; Pu, Y. N.; Qi, M.; Qian, S.; Qiao, C. F.; Qin, L. Q.; Qin, N.; Qin, X. S.; Qin, Y.; Qin, Z. H.; Qiu, J. F.; Rashid, K. H.; Redmer, C. F.; Ren, H. L.; Ripka, M.; Rong, G.; Ruan, X. D.; Santoro, V.; Sarantsev, A.; Savrie, M.; Schoenning, K.; Schumann, S.; Shan, W.; Shao, M.; Shen, C. P.; Shen, P. X.; Shen, X. Y.; Sheng, H. Y.; Shepherd, M. R.; Song, W. M.; Song, X. Y.; Sosio, S.; Spataro, S.; Spruck, B.; Sun, G. X.; Sun, J. F.; Sun, S. S.; Sun, Y. J.; Sun, Y. Z.; Sun, Z. J.; Sun, Z. T.; Tang, C. J.; Tang, X.; Tapan, I.; Thorndike, E. H.; Tiemens, M.; Toth, D.; Ullrich, M.; Uman, I.; Varner, G. S.; Wang, B.; Wang, B. L.; Wang, D.; Wang, D. Y.; Wang, K.; Wang, L. L.; Wang, L. S.; Wang, M.; Wang, P.; Wang, P. L.; Wang, Q. J.; Wang, S. G.; Wang, W.; Wang, X. F.; Wang, Y. D.; Wang, Y. F.; Wang, Y. Q.; Wang, Z.; Wang, Z. G.; Wang, Z. H.; Wang, Z. Y.; Wei, D. H.; Wei, J. B.; Weidenkaff, P.; Wen, S. P.; Wiedner, U.; Wolke, M.; Wu, L. H.; Wu, Z.; Xia, L. G.; Xia, Y.; Xiao, D.; Xiao, Z. J.; Xie, Y. G.; Xiu, Q. L.; Xu, G. F.; Xu, L.; Xu, Q. J.; Xu, Q. N.; Xu, X. P.; Yan, L.; Yan, W. B.; Yan, W. C.; Yan, Y. H.; Yang, H. X.; Yang, L.; Yang, Y.; Yang, Y. X.; Ye, H.; Ye, M.; Ye, M. H.; Yin, J. H.; Yu, B. X.; Yu, C. X.; Yu, H. W.; Yu, J. S.; Yuan, C. Z.; Yuan, W. L.; Yuan, Y.; Yuncu, A.; Zafar, A. A.; Zallo, A.; Zeng, Y.; Zhang, B. X.; Zhang, B. Y.; Zhang, C.; Zhang, C. C.; Zhang, D. H.; Zhang, H. H.; Zhang, H. Y.; Zhang, J. J.; Zhang, J. L.; Zhang, J. Q.; Zhang, J. W.; Zhang, J. Y.; Zhang, J. Z.; Zhang, K.; Zhang, L.; Zhang, S. H.; Zhang, X. J.; Zhang, X. Y.; Zhang, Y.; Zhang, Y. H.; Zhang, Z. H.; Zhang, Z. P.; Zhang, Z. Y.; Zhao, G.; Zhao, J. W.; Zhao, J. Y.; Zhao, J. Z.; Zhao, Lei; Zhao, Ling; Zhao, M. G.; Zhao, Q.; Zhao, Q. W.; Zhao, S. J.; Zhao, T. C.; Zhao, Y. B.; Zhao, Z. G.; Zhemchugov, A.; Zheng, B.; Zheng, J. P.; Zheng, W. J.; Zheng, Y. H.; Zhong, B.; Zhou, L.; Zhou, Li; Zhou, X.; Zhou, X. K.; Zhou, X. R.; Zhou, X. Y.; Zhu, K.; Zhu, K. J.; Zhu, S.; Zhu, X. L.; Zhu, Y. C.; Zhu, Y. S.; Zhu, Z. A.; Zhuang, J.; Zou, B. S.; Zou, J. H.

    2014-01-01

    Using a sample of 2.25 x 10(8) J/psi events collected with the BESIII detector at the BEPCII collider, we search for the J/psi semileptonic weak decay J/psi -> D-s(-) e(+)nu(e) +c.c. with a much higher sensitivity than previous searches. We also perform the first search for J/psi -> D-s(*-) e(+) nu(

  20. Transfer Hydrogenation of C= C Double Bonds Catalyzed by Ruthenium Amido-Complexes:Scopes, Limitation and Enantioselectivity

    Institute of Scientific and Technical Information of China (English)

    XUE,Dong; CHENG,Ying-Chun; CUI,Xin; WANG,Qi-Wei; ZHU,Jin; DENG,Jin-Gen

    2004-01-01

    @@ The reduction of C = C double bonds is one of the most fundamental synthetic transformations and plays a key role in the manufacturing of a wide variety of bulk and fine chemicals. Hydrogenation of olefinic substrates can be achieved readily with molecular hydrogen in many cases, but transfer hydrogenation methods using suitable donor molecules such as formic acid or alcohols are receiving increasing attention as possible synthetic alternatives because it requires no special equipment and avoids the handling of potentially hazardous gaseous hydrogen.

  1. Pd/C-mediated dual C-C bond forming reaction in water: synthesis of 2,4-dialkynylquinoline

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Ellanki A.; Islam, Aminul; Venu, Bolla K. [Dr. Reddy' s Laboratories Limited, Hyderabad, Andhra Pradesh (India); Mukkanti, K. [JNT University, Hyderabad, Andhra Pradesh (India). Inst. of Science and Technology. Chemistry Division; Pal, Manojit, E-mail: manojitpal@rediffmail.co [Matrix Laboratories Ltd., Medak District, Andra Pradesh (India). New Drug Discovery. R and D Center

    2010-07-01

    Pd/C facilitated dual C-C bond forming reaction between 2,4-diiodoquinoline and terminal alkynes in water providing a practical and one-step synthesis of 2,4-dialkynylquinolines. A number of related quinoline derivatives were prepared in good to excellent yields using this water-based methodology. The use of other palladium catalysts and solvents was examined and the mechanism of the reaction has been discussed. (author)

  2. The use of ultrasmall iron(0) nanoparticles as catalysts for the selective hydrogenation of unsaturated C-C bonds.

    Science.gov (United States)

    Kelsen, Vinciane; Wendt, Bianca; Werkmeister, Svenja; Junge, Kathrin; Beller, Matthias; Chaudret, Bruno

    2013-04-28

    The performance of well-defined ultrasmall iron(0) nanoparticles (NPs) as catalysts for the selective hydrogenation of unsaturated C-C and C=X bonds is reported. Monodisperse iron nanoparticles of about 2 nm size are synthesized by the decomposition of {Fe(N[Si(CH3)3]2)2}2 under dihydrogen. They are found to be active for the hydrogenation of various alkenes and alkynes under mild conditions and weakly active for C=O bond hydrogenation.

  3. Effects of Preform Density on Structure and Property of C/C-SiC Composites Fabricated by Gaseous Silicon Infiltration

    Directory of Open Access Journals (Sweden)

    CAO Yu

    2016-07-01

    Full Text Available The 3-D needled C/C preforms with different densities deposited by chemical vapor infiltration (CVI method were used to fabricate C/C-SiC composites by gaseous silicon infiltration (GSI. The porosity and CVI C thickness of the preforms were studied, and the effects of preform density on the mechanical and thermal properties of C/C-SiC composites were analyzed. The results show that with the increase of preform density, the preform porosity decreases and the CVI C thickness increases from several hundred nanometers to several microns. For the C/C-SiC composites, as the preform density increases, the residual C content increases while the density and residual Si content decreases. The SiC content first keeps at a high level of about 40% (volume fraction, which then quickly reduces. Meanwhile, the mechanical properties increase to the highest values when the preform density is 1.085g/cm3, with the flexure strength up to 308.31MP and fracture toughness up to 11.36MPa·m1/2, which then decrease as the preform density further increases. The thermal conductivity and CTE of the composites, however, decrease with the increase of preform density. It is found that when the preform porosity is too high, sufficient infiltration channels lead to more residual Si, and thinner CVI C thickness results in the severe corrosion of the reinforcing fibers by Si and lower mechanical properties. When the preform porosity is relatively low, the contents of Si and SiC quickly reduce since the infiltration channels are rapidly blocked, resulting in the formation of large closed pores and not high mechanical properties.

  4. Chiral BINOL-derived phosphoric acids: privileged Brønsted acid organocatalysts for C-C bond formation reactions.

    Science.gov (United States)

    Zamfir, Alexandru; Schenker, Sebastian; Freund, Matthias; Tsogoeva, Svetlana B

    2010-12-07

    BINOL-derived phosphoric acids have emerged during the last five years as powerful chiral Brønsted acid catalysts in many enantioselective processes. The most successful transformations carried out with chiral BINOL phosphates include C-C bond formation reactions. The recent advances have been reviewed in this article with a focus being placed on hydrocyanations, aldol-type, Mannich, Friedel-Crafts, aza-ene-type, Diels-Alder, as well as cascade and multi-component reactions.

  5. CCR2 knockout exacerbates cerulein-induced chronic pancreatitis with hyperglycemia via decreased GLP-1 receptor expression and insulin secretion.

    Science.gov (United States)

    Nakamura, Yuji; Kanai, Takanori; Saeki, Keita; Takabe, Miho; Irie, Junichiro; Miyoshi, Jun; Mikami, Yohei; Teratani, Toshiaki; Suzuki, Takahiro; Miyata, Naoteru; Hisamatsu, Tadakazu; Nakamoto, Nobuhiro; Yamagishi, Yoshiyuki; Higuchi, Hajime; Ebinuma, Hirotoshi; Hozawa, Shigenari; Saito, Hidetsugu; Itoh, Hiroshi; Hibi, Toshifumi

    2013-04-15

    Glucagon-like peptide-1 (GLP-1) promotes insulin release; however, the relationship between the GLP-1 signal and chronic pancreatitis is not well understood. Here we focus on chemokine (C-C motif) ligand 2 (CCL2) and its receptor (CCR2) axis, which regulates various immune cells, including macrophages, to clarify the mechanism of GLP-1-mediated insulin secretion in chronic pancreatitis in mice. One and multiple series of repetitive cerulein administrations were used to induce acute and chronic cerulein pancreatitis, respectively. Acute cerulein-administered CCR2-knockout (KO) mice showed suppressed infiltration of CD11b(+)Gr-1(low) macrophages and pancreatic inflammation and significantly upregulated insulin secretion compared with paired wild-type (WT) mice. However, chronic cerulein-administered CCR2-KO mice showed significantly increased infiltration of CD11b(+)/Gr-1(-) and CD11b(+)/Gr-1(high) cells, but not CD11b(+)/Gr-1(low) cells, in pancreas with severe inflammation and significantly decreased insulin secretion compared with their WT counterparts. Furthermore, although serum GLP-1 levels in chronic cerulein-administered WT and CCR2-KO mice were comparably upregulated after cerulein administrations, GLP-1 receptor levels in pancreases of chronic cerulein-administered CCR2-KO mice were significantly lower than in paired WT mice. Nevertheless, a significantly higher hyperglycemia level in chronic cerulein-administered CCR2-KO mice was markedly restored by treatment with a GLP-1 analog to a level comparable to the paired WT mice. Collectively, the CCR2/CCL2 axis-mediated CD11b(+)-cell migration to the pancreas is critically involved in chronic pancreatitis-mediated hyperglycemia through the modulation of GLP-1 receptor expression and insulin secretion.

  6. Cu6Sn5-TiC-C nanocomposite anodes for high-performance sodium-ion batteries

    Science.gov (United States)

    Kim, Il Tae; Allcorn, Eric; Manthiram, Arumugam

    2015-05-01

    Cu6Sn5 alloy nanoparticles dispersed in a TiC and C conductive matrix have been developed via high energy mechanical milling (HEMM), and the resulting Cu6Sn5-TiC-C nanocomposite has been assessed as anodes for sodium-ion batteries. Composite anodes of Sn-C exhibit poor cyclic performance even with the introduction of 2 vol. % fluoroethylene carbonate (FEC) additive into the electrolyte. In contrast, Cu6Sn5-TiC-C nanocomposite anodes exhibit stable cycle life corresponding to a capacity retention of ∼80% at 40 cycles and high-rate performance with a capacity retention of ∼62% at 3000 mA g-1. These superior performance metrics is ascribed to the well-developed electrochemically active nanocrystalline material (Cu6Sn5) as well as a hybrid conductive matrix (TiC and C). The incorporation of 2 vol. % FEC additive into the electrolyte further improves the performance of Cu6Sn5-TiC-C nanocomposite to display a capacity retention of ∼94% at 250 cycles and high-rate capacity retention of ∼82% at 5000 mA g-1, which are attributed to the formation of a thin and stable SEI layer in presence of FEC.

  7. A method of quantitative characterization for the component of C/C composites based on the PLM video

    Science.gov (United States)

    Li, Y. X.; Qi, L. H.; Song, Y. S.; Li, H. J.

    2016-07-01

    PLM video is used for studying the microstructure of C/C composites, because it contains the structure and motion information at the same time. It means that PLM video could provide more comprehensive microstructure features of C/C composites, and then the microstructure could be quantitatively characterized by image processing. However, several unavoidable displacements still exist in the PLM video, which could occur during the process of image acquisition. Therefore, an image registration method was put forward to correct the displacements by the phase correlation, and further to achieve the quantitative characterization of component combined with image fusion and threshold segmentation based on the PLM video of C/C composites. Specifically, PLM video was decomposed to a frame sequence firstly. Then a series of processes was carried out on this basis, including selecting the frame as equal interval, segmenting the static and dynamic regions and correcting the relative displacements between the adjacent frames. Meanwhile, the result of image registration was verified through image fusion, and it indicates that the proposed method could eliminate the displacements effectively. Finally, some operations of image processing were used to segment the components and calculate their fractions, thus the quantitative calculation was achieved successfully.

  8. DNA nanotechnology based on i-motif structures.

    Science.gov (United States)

    Dong, Yuanchen; Yang, Zhongqiang; Liu, Dongsheng

    2014-06-17

    CONSPECTUS: Most biological processes happen at the nanometer scale, and understanding the energy transformations and material transportation mechanisms within living organisms has proved challenging. To better understand the secrets of life, researchers have investigated artificial molecular motors and devices over the past decade because such systems can mimic certain biological processes. DNA nanotechnology based on i-motif structures is one system that has played an important role in these investigations. In this Account, we summarize recent advances in functional DNA nanotechnology based on i-motif structures. The i-motif is a DNA quadruplex that occurs as four stretches of cytosine repeat sequences form C·CH(+) base pairs, and their stabilization requires slightly acidic conditions. This unique property has produced the first DNA molecular motor driven by pH changes. The motor is reliable, and studies show that it is capable of millisecond running speeds, comparable to the speed of natural protein motors. With careful design, the output of these types of motors was combined to drive micrometer-sized cantilevers bend. Using established DNA nanostructure assembly and functionalization methods, researchers can easily integrate the motor within other DNA assembled structures and functional units, producing DNA molecular devices with new functions such as suprahydrophobic/suprahydrophilic smart surfaces that switch, intelligent nanopores triggered by pH changes, molecular logic gates, and DNA nanosprings. Recently, researchers have produced motors driven by light and electricity, which have allowed DNA motors to be integrated within silicon-based nanodevices. Moreover, some devices based on i-motif structures have proven useful for investigating processes within living cells. The pH-responsiveness of the i-motif structure also provides a way to control the stepwise assembly of DNA nanostructures. In addition, because of the stability of the i-motif, this

  9. Analysis of septins across kingdoms reveals orthology and new motifs

    Directory of Open Access Journals (Sweden)

    Malmberg Russell L

    2007-07-01

    Full Text Available Abstract Background Septins are cytoskeletal GTPase proteins first discovered in the fungus Saccharomyces cerevisiae where they organize the septum and link nuclear division with cell division. More recently septins have been found in animals where they are important in processes ranging from actin and microtubule organization to embryonic patterning and where defects in septins have been implicated in human disease. Previous studies suggested that many animal septins fell into independent evolutionary groups, confounding cross-kingdom comparison. Results In the current work, we identified 162 septins from fungi, microsporidia and animals and analyzed their phylogenetic relationships. There was support for five groups of septins with orthology between kingdoms. Group 1 (which includes S. cerevisiae Cdc10p and human Sept9 and Group 2 (which includes S. cerevisiae Cdc3p and human Sept7 contain sequences from fungi and animals. Group 3 (which includes S. cerevisiae Cdc11p and Group 4 (which includes S. cerevisiae Cdc12p contain sequences from fungi and microsporidia. Group 5 (which includes Aspergillus nidulans AspE contains sequences from filamentous fungi. We suggest a modified nomenclature based on these phylogenetic relationships. Comparative sequence alignments revealed septin derivatives of already known G1, G3 and G4 GTPase motifs, four new motifs from two to twelve amino acids long and six conserved single amino acid positions. One of these new motifs is septin-specific and several are group specific. Conclusion Our studies provide an evolutionary history for this important family of proteins and a framework and consistent nomenclature for comparison of septin orthologs across kingdoms.

  10. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  11. Sequence-based classification using discriminatory motif feature selection.

    Directory of Open Access Journals (Sweden)

    Hao Xiong

    Full Text Available Most existing methods for sequence-based classification use exhaustive feature generation, employing, for example, all k-mer patterns. The motivation behind such (enumerative approaches is to minimize the potential for overlooking important features. However, there are shortcomings to this strategy. First, practical constraints limit the scope of exhaustive feature generation to patterns of length ≤ k, such that potentially important, longer (> k predictors are not considered. Second, features so generated exhibit strong dependencies, which can complicate understanding of derived classification rules. Third, and most importantly, numerous irrelevant features are created. These concerns can compromise prediction and interpretation. While remedies have been proposed, they tend to be problem-specific and not broadly applicable. Here, we develop a generally applicable methodology, and an attendant software pipeline, that is predicated on discriminatory motif finding. In addition to the traditional training and validation partitions, our framework entails a third level of data partitioning, a discovery partition. A discriminatory motif finder is used on sequences and associated class labels in the discovery partition to yield a (small set of features. These features are then used as inputs to a classifier in the training partition. Finally, performance assessment occurs on the validation partition. Important attributes of our approach are its modularity (any discriminatory motif finder and any classifier can be deployed and its universality (all data, including sequences that are unaligned and/or of unequal length, can be accommodated. We illustrate our approach on two nucleosome occupancy datasets and a protein solubility dataset, previously analyzed using enumerative feature generation. Our method achieves excellent performance results, with and without optimization of classifier tuning parameters. A Python pipeline implementing the approach is

  12. Nod factor receptors form heteromeric complexes and are essential for intracellular infection in Medicago nodules

    NARCIS (Netherlands)

    Moling, S.; Pietraszewska-Bogiel, A.; Postma, M.; Fedorova, E.E.; Hink, M.A.; Limpens, E.H.M.; Gadella, T.W.J.; Bisseling, T.

    2014-01-01

    Rhizobial Nod factors are the key signaling molecules in the legume-rhizobium nodule symbiosis. In this study, the role of the Nod factor receptors NOD FACTOR PERCEPTION (NFP) and LYSIN MOTIF RECEPTOR-LIKE KINASE3 (LYK3) in establishing the symbiotic interface in root nodules was investigated. It wa

  13. Nod factor receptors form heteromeric complexes and are essential for intracellular infection in medicago nodules

    NARCIS (Netherlands)

    Moling, S.; Pietraszewska-Bogiel, A.; Postma, M.; Fedorova, E.; Hink, M.A.; Limpens, E.; Gadella, T.W.J.; Bisseling, T.

    2014-01-01

    Rhizobial Nod factors are the key signaling molecules in the legume-rhizobium nodule symbiosis. In this study, the role of the Nod factor receptors NOD FACTOR PERCEPTION (NFP) and LYSIN MOTIF RECEPTOR-LIKE KINASE3 (LYK3) in establishing the symbiotic interface in root nodules was investigated. It wa

  14. Mouse mutants for the nicotinic acetylcholine receptor ß2 subunit display changes in cell adhesion and neurodegeneration response genes.

    Directory of Open Access Journals (Sweden)

    Carol M Rubin

    Full Text Available Mice lacking expression of the ß2 subunit of the neuronal nicotinic acetylcholine receptor (CHRNB2 display abnormal retinal waves and a dispersed projection of retinal ganglion cell (RGC axons to their dorsal lateral geniculate nuclei (dLGNs. Transcriptomes of LGN tissue from two independently generated Chrnb2-/- mutants and from wildtype mice were obtained at postnatal day 4 (P4, during the normal period of segregation of eye-specific afferents to the LGN. Microarray analysis reveals reduced expression of genes located on the cell membrane or in extracellular space, and of genes active in cell adhesion and calcium signaling. In particular, mRNA for cadherin 1 (Cdh1, a known axon growth regulator, is reduced to nearly undetectable levels in the LGN of P4 mutant mice and Lypd2 mRNA is similarly suppressed. Similar analysis of retinal tissue shows increased expression of crumbs 1 (Crb1 and chemokine (C-C motif ligand 21 (Ccl21 mRNAs in Chrnb2-/- mutant animals. Mutations in these genes are associated with retinal neuronal degeneration. The retinas of Chrnb2-/- mutants are normal in appearance, but the increased expression of these genes may also be involved in the abnormal projection patterns of RGC to the LGN. These data may provide the tools to distinguish the interplay between neural activity and molecular expression. Finally, comparison of the transcriptomes of the two different Chrnb2-/- mutant strains reveals the effects of genetic background upon gene expression.

  15. Indonesian Traditional Toys and the Development of Batik Motifs

    Directory of Open Access Journals (Sweden)

    Bagus Indrayana

    2016-06-01

    Full Text Available There is a wide array of traditional toys in Indonesia. In the past, traditional toys played an important role for skill and creativity development of children. Today, the position of traditional toys in the society is displaced by toys from large-scale manufacturers. Given the critical role of traditional toys for children’s motoric and social development, there is a need to develop media that can be used to promote these traditional products and strengthen their position in the public. We propose to use Batik as a way to effectively disseminate and promote traditional toys to the general public. Apart from this, using traditional toys to create new Batik motifs can have an economic value for the producers of Batik, promote Indonesian products and enrich the Indonesian Batik. This study aims to explore the variety of traditional toys, mainly from Klaten and Magelang, in the Central Java province of Indonesia, and use them as the basis for the development of Batik motif creation. This study used Trilogi Keseimbangan (or Harmony Trilogy aesthetic theory analytical approach that explains the creation of craft consists of the following phases: exploration, design, and materialization. The creation method in this study adopts Tiga Tahap Enam Langkah (Three Phases, Six Steps method offered in the theory. The finding in the field found that the traditional toys material used in Klaten and Magelang, mostly made from waste wood, plywood, and zinc. The manufacturing process is done manually by two or three craftsmen using a simple technology. The traditional toys are designed by the artisans mostly, although there may be designs from the clients. In addition, we also found that the traditional toys have never been used as a Batik motif. The traditional toys Batik motif presented in this work is researcher’s design. For the purposes of this study, we first research the variety of traditional toys available in the market today in Indonesia. We look

  16. Core signalling motif displaying multistability through multi-state enzymes

    DEFF Research Database (Denmark)

    Feng, Song; Saez Cornellana, Meritxell; Wiuf, Carsten Henrik

    2016-01-01

    Bistability, and more generally multistability, is a key system dynamics feature enabling decision-making and memory in cells. Deciphering the molecular determinants of multistability is thus crucial for a better understanding of cellular pathways and their (re)engineering in synthetic biology......-state kinases and the described competition-based motif are part of several natural signalling systems and thereby could enable them to implement complex information processing through multistability. These results indicate that multi-state kinases in signalling systems are readily exploited by natural...

  17. Discovering sequence motifs in quantitative and qualitative pepetide data

    DEFF Research Database (Denmark)

    Andreatta, Massimo

    -dimensional, as binding sites normally consist of a pocket or a groove on the protein surface. However, in many cases such interactions contain a linear component and can be more conveniently represented, or approximated, by a protein-peptide interaction. Whereas time-consuming structural studies are necessary in systems...... and interpret such data. The first paper in this thesis presents a new, publicly available method based on artificial neural networks that allows custom analysis of quantitative peptide data. The online NNAlign web-server provides a simple yet powerful tool for the discovery of sequence motifs in large...

  18. Nucleic Acid i-Motif Structures in Analytical Chemistry.

    Science.gov (United States)

    Alba, Joan Josep; Sadurní, Anna; Gargallo, Raimundo

    2016-09-02

    Under the appropriate experimental conditions of pH and temperature, cytosine-rich segments in DNA or RNA sequences may produce a characteristic folded structure known as an i-motif. Besides its potential role in vivo, which is still under investigation, this structure has attracted increasing interest in other fields due to its sharp, fast and reversible pH-driven conformational changes. This "on/off" switch at molecular level is being used in nanotechnology and analytical chemistry to develop nanomachines and sensors, respectively. This paper presents a review of the latest applications of this structure in the field of chemical analysis.

  19. Present status of quinoxaline motifs: excellent pathfinders in therapeutic medicine.

    Science.gov (United States)

    Ajani, Olayinka Oyewale

    2014-10-01

    Quinoxalines belong to a class of excellent heterocyclic scaffolds owing to their wide biological properties and diverse therapeutic applications in medicinal research. They are complementary in shapes and charges to numerous biomolecules they interact with, thereby resulting in increased binding affinity. The pharmacokinetic properties of drugs bearing quinoxaline cores have shown them to be relatively easy to administer either as intramuscular solutions, oral capsules or rectal suppositories. This work deals with recent advances in the synthesis and pharmacological diversities of quinoxaline motifs which might pave ways for novel drugs development.

  20. Evolving DNA motifs to predict GeneChip probe performance

    Directory of Open Access Journals (Sweden)

    Harrison AP

    2009-03-01

    Full Text Available Abstract Background Affymetrix High Density Oligonuclotide Arrays (HDONA simultaneously measure expression of thousands of genes using millions of probes. We use correlations between measurements for the same gene across 6685 human tissue samples from NCBI's GEO database to indicated the quality of individual HG-U133A probes. Low correlation indicates a poor probe. Results Regular expressions can be automatically created from a Backus-Naur form (BNF context-free grammar using strongly typed genetic programming. Conclusion The automatically produced motif is better at predicting poor DNA sequences than an existing human generated RE, suggesting runs of Cytosine and Guanine and mixtures should all be avoided.

  1. Alignment of capsid protein VP1 sequences of all human rhinovirus prototype strains: conserved motifs and functional domains.

    Science.gov (United States)

    Laine, Pia; Blomqvist, Soile; Savolainen, Carita; Andries, Koen; Hovi, Tapani

    2006-01-01

    An alignment was made of the deduced amino acid sequences of the entire capsid protein VP1 of all human rhinovirus (HRV) prototype strains to examine conserved motifs in the primary structure. A set of previously proposed crucially important amino acids in the footprints of the two known receptor molecules was not conserved in a receptor group-specific way. In contrast, VP1 and VP3 amino acids in the minor receptor-group strains corresponding to most of the predicted ICAM-1 footprint definitely differed from those of the ICAM-1-using major receptor-group strains. Previous antiviral-sensitivity classification showed an almost-complete agreement with the species classification and a fair correlation with amino acids aligning in the antiviral pocket. It was concluded that systematic alignment of sequences of related virus strains can be used to test hypotheses derived from molecular studies of individual model viruses and to generate ideas for future studies on virus structure and replication.

  2. New horizons for lipoprotein receptors

    DEFF Research Database (Denmark)

    Andersen, Olav M.; Dagil, Robert; Kragelund, Birthe Brandt

    2013-01-01

    , this dogma has transformed with the observation that β-propellers of some LRs actively engage in complex formation too. Based on an in-depth decomposition of current structures and sequences, we suggest that exploitation of the β-propellers as binding targets depends on receptor subgroups. In particular, we...... highlight the shutter mechanism of β-propellers as a general recognition motif for NxI-containing ligands, and we present indications that the generalized β-propeller-induced ligand release mechanism is not applicable for the larger LRs. For the giant LR members, we present evidence that their β-propellers...

  3. Observations on the ligand selectivity of the melanocortin 2 receptor.

    Science.gov (United States)

    Veo, Kristopher; Reinick, Christina; Liang, Liang; Moser, Emily; Angleson, Joseph K; Dores, Robert M

    2011-05-15

    The melanocortin 2 receptor (MC2R) is unique in terms of ligand selectivity and in vitro expression in mammalian cell lines as compared to the other four mammalian MCRs. It is well established that ACTH is the only melanocortin ligand that can activate the ACTH receptor (i.e., melanocortin 2 receptor). Recent studies have provided new insights into the presence of a common binding site for the HFRW motif common to all melanocortin ligands. However, the activation of the melanocortin 2 receptor requires an additional amino acid motif that is only found in the sequence of ACTH. This mini-review will focus on these two topics and provide a phylogenetic perspective on the evolution of MC2R ligand selectivity.

  4. Fast and Accurate Discovery of Degenerate Linear Motifs in Protein Sequences

    Science.gov (United States)

    Levy, Emmanuel D.; Michnick, Stephen W.

    2014-01-01

    Linear motifs mediate a wide variety of cellular functions, which makes their characterization in protein sequences crucial to understanding cellular systems. However, the short length and degenerate nature of linear motifs make their discovery a difficult problem. Here, we introduce MotifHound, an algorithm particularly suited for the discovery of small and degenerate linear motifs. MotifHound performs an exact and exhaustive enumeration of all motifs present in proteins of interest, including all of their degenerate forms, and scores the overrepresentation of each motif based on its occurrence in proteins of interest relative to a background (e.g., proteome) using the hypergeometric distribution. To assess MotifHound, we benchmarked it together with state-of-the-art algorithms. The benchmark consists of 11,880 sets of proteins from S. cerevisiae; in each set, we artificially spiked-in one motif varying in terms of three key parameters, (i) number of occurrences, (ii) length and (iii) the number of degenerate or “wildcard” positions. The benchmark enabled the evaluation of the impact of these three properties on the performance of the different algorithms. The results showed that MotifHound and SLiMFinder were the most accurate in detecting degenerate linear motifs. Interestingly, MotifHound was 15 to 20 times faster at comparable accuracy and performed best in the discovery of highly degenerate motifs. We complemented the benchmark by an analysis of proteins experimentally shown to bind the FUS1 SH3 domain from S. cerevisiae. Using the full-length protein partners as sole information, MotifHound recapitulated most experimentally determined motifs binding to the FUS1 SH3 domain. Moreover, these motifs exhibited properties typical of SH3 binding peptides, e.g., high intrinsic disorder and evolutionary conservation, despite the fact that none of these properties were used as prior information. MotifHound is available (http://michnick.bcm.umontreal.ca or http

  5. Chemokine CCL2 and its receptor CCR2 in the medullary dorsal horn are involved in trigeminal neuropathic pain

    Directory of Open Access Journals (Sweden)

    Zhang Zhi-Jun

    2012-07-01

    Full Text Available Abstract Background Neuropathic pain in the trigeminal system is frequently observed in clinic, but the mechanisms involved are largely unknown. In addition, the function of immune cells and related chemicals in the mechanism of pain has been recognized, whereas few studies have addressed the potential role of chemokines in the trigeminal system in chronic pain. The present study was undertaken to test the hypothesis that chemokine C-C motif ligand 2 (CCL2-chemokine C-C motif receptor 2 (CCR2 signaling in the trigeminal nucleus is involved in the maintenance of trigeminal neuropathic pain. Methods The inferior alveolar nerve and mental nerve transection (IAMNT was used to induce trigeminal neuropathic pain. The expression of ATF3, CCL2, glial fibrillary acidic protein (GFAP, and CCR2 were detected by immunofluorescence histochemical staining and western blot. The cellular localization of CCL2 and CCR2 were examined by immunofluorescence double staining. The effect of a selective CCR2 antagonist, RS504393 on pain hypersensitivity was checked by behavioral testing. Results IAMNT induced persistent (>21 days heat hyperalgesia of the orofacial region and ATF3 expression in the mandibular division of the trigeminal ganglion. Meanwhile, CCL2 expression was increased in the medullary dorsal horn (MDH from 3 days to 21 days after IAMNT. The induced CCL2 was colocalized with astroglial marker GFAP, but not with neuronal marker NeuN or microglial marker OX-42. Astrocytes activation was also found in the MDH and it started at 3 days, peaked at 10 days and maintained at 21 days after IAMNT. In addition, CCR2 was upregulated by IAMNT in the ipsilateral medulla and lasted for more than 21 days. CCR2 was mainly colocalized with NeuN and few cells were colocalized with GFAP. Finally, intracisternal injection of CCR2 antagonist, RS504393 (1, 10 μg significantly attenuated IAMNT-induced heat hyperalgesia. Conclusion The data suggest that CCL2-CCR

  6. Transcription factor motif quality assessment requires systematic comparative analysis [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Caleb Kipkurui Kibet

    2016-03-01

    Full Text Available Transcription factor (TF binding site prediction remains a challenge in gene regulatory research due to degeneracy and potential variability in binding sites in the genome. Dozens of algorithms designed to learn binding models (motifs have generated many motifs available in research papers with a subset making it to databases like JASPAR, UniPROBE and Transfac. The presence of many versions of motifs from the various databases for a single TF and the lack of a standardized assessment technique makes it difficult for biologists to make an appropriate choice of binding model and for algorithm developers to benchmark, test and improve on their models. In this study, we review and evaluate the approaches in use, highlight differences and demonstrate the difficulty of defining a standardized motif assessment approach. We review scoring functions, motif length, test data and the type of performance metrics used in prior studies as some of the factors that influence the outcome of a motif assessment. We show that the scoring functions and statistics used in motif assessment influence ranking of motifs in a TF-specific manner. We also show that TF binding specificity can vary by source of genomic binding data. We also demonstrate that information content of a motif is not in isolation a measure of motif quality but is influenced by TF binding behaviour. We conclude that there is a need for an easy-to-use tool that presents all available evidence for a comparative analysis.

  7. Finding a Leucine in a Haystack: Searching the Proteome for ambigous Leucine-Aspartic Acid motifs

    KAUST Repository

    Arold, Stefan T.

    2016-01-25

    Leucine-aspartic acid (LD) motifs are short helical protein-protein interaction motifs involved in cell motility, survival and communication. LD motif interactions are also implicated in cancer metastasis and are targeted by several viruses. LD motifs are notoriously difficult to detect because sequence pattern searches lead to an excessively high number of false positives. Hence, despite 20 years of research, only six LD motif–containing proteins are known in humans, three of which are close homologues of the paxillin family. To enable the proteome-wide discovery of LD motifs, we developed LD Motif Finder (LDMF), a web tool based on machine learning that combines sequence information with structural predictions to detect LD motifs with high accuracy. LDMF predicted 13 new LD motifs in humans. Using biophysical assays, we experimentally confirmed in vitro interactions for four novel LD motif proteins. Thus, LDMF allows proteome-wide discovery of LD motifs, despite a highly ambiguous sequence pattern. Functional implications will be discussed.

  8. Motif Discovery in Tissue-Specific Regulatory Sequences Using Directed Information

    Directory of Open Access Journals (Sweden)

    States David

    2007-01-01

    Full Text Available Motif discovery for the identification of functional regulatory elements underlying gene expression is a challenging problem. Sequence inspection often leads to discovery of novel motifs (including transcription factor sites with previously uncharacterized function in gene expression. Coupled with the complexity underlying tissue-specific gene expression, there are several motifs that are putatively responsible for expression in a certain cell type. This has important implications in understanding fundamental biological processes such as development and disease progression. In this work, we present an approach to the identification of motifs (not necessarily transcription factor sites and examine its application to some questions in current bioinformatics research. These motifs are seen to discriminate tissue-specific gene promoter or regulatory regions from those that are not tissue-specific. There are two main contributions of this work. Firstly, we propose the use of directed information for such classification constrained motif discovery, and then use the selected features with a support vector machine (SVM classifier to find the tissue specificity of any sequence of interest. Such analysis yields several novel interesting motifs that merit further experimental characterization. Furthermore, this approach leads to a principled framework for the prospective examination of any chosen motif to be discriminatory motif for a group of coexpressed/coregulated genes, thereby integrating sequence and expression perspectives. We hypothesize that the discovery of these motifs would enable the large-scale investigation for the tissue-specific regulatory role of any conserved sequence element identified from genome-wide studies.

  9. Transduction motif analysis of gastric cancer based on a human signaling network

    Energy Technology Data Exchange (ETDEWEB)

    Liu, G.; Li, D.Z.; Jiang, C.S.; Wang, W. [Fuzhou General Hospital of Nanjing Command, Department of Gastroenterology, Fuzhou, China, Department of Gastroenterology, Fuzhou General Hospital of Nanjing Command, Fuzhou (China)

    2014-04-04

    To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs in a network with three vertices. The significant motif difference method was adopted to identify significantly different motifs in the normal and cancer states. Finally, we conducted a series of analyses of the significantly different motifs, including gene ontology, function annotation of genes, and model classification. A human signaling network was constructed, with 1643 nodes and 5089 regulating interactions. The network was configured to have the characteristics of other biological networks. There were 57,942 motifs marked with gastric cancer-related genes out of a total of 69,492 motifs, and 264 motifs were selected as significantly different motifs by calculating the significant motif difference (SMD) scores. Genes in significantly different motifs were mainly enriched in functions associated with cancer genesis, such as regulation of cell death, amino acid phosphorylation of proteins, and intracellular signaling cascades. The top five significantly different motifs were mainly cascade and positive feedback types. Almost all genes in the five motifs were cancer related, including EPOR, MAPK14, BCL2L1, KRT18, PTPN6, CASP3, TGFBR2, AR, and CASP7. The development of cancer might be curbed by inhibiting signal transductions upstream and downstream of the selected motifs.

  10. Dopamine receptor-interacting protein 78 acts as a molecular chaperone for CCR5 chemokine receptor signaling complex organization.

    Directory of Open Access Journals (Sweden)

    Yi-Qun Kuang

    Full Text Available Chemokine receptors are members of the G protein-coupled receptor (GPCR family. CCR5 and CXCR4 act as co-receptors for human immunodeficiency virus (HIV and several efforts have been made to develop ligands to inhibit HIV infection by blocking those receptors. Removal of chemokine receptors from the cell surface using polymorphisms or other means confers some levels of immunity against HIV infection. Up to now, very limited success has been obtained using ligand therapies so we explored potential avenues to regulate chemokine receptor expression at the plasma membrane. We identified a molecular chaperone, DRiP78, that interacts with both CXCR4 and CCR5, but not the heterodimer formed by these receptors. We further characterized the effects of DRiP78 on CCR5 function. We show that the molecular chaperone inhibits CCR5 localization to the plasma membrane. We identified the interaction region on the receptor, the F(x6LL motif, and show that upon mutation of this motif the chaperone cannot interact with the receptor. We also show that DRiP78 is involved in the assembly of CCR5 chemokine signaling complex as a homodimer, as well as with the Gαi protein. Finally, modulation of DRiP78 levels will affect receptor functions, such as cell migration in cells that endogenously express CCR5. Our results demonstrate that modulation of the functions of a chaperone can affect signal transduction at the cell surface.

  11. Dopamine receptor-interacting protein 78 acts as a molecular chaperone for CCR5 chemokine receptor signaling complex organization.

    Science.gov (United States)

    Kuang, Yi-Qun; Charette, Nicholle; Frazer, Jennifer; Holland, Patrick J; Attwood, Kathleen M; Dellaire, Graham; Dupré, Denis J

    2012-01-01

    Chemokine receptors are members of the G protein-coupled receptor (GPCR) family. CCR5 and CXCR4 act as co-receptors for human immunodeficiency virus (HIV) and several efforts have been made to develop ligands to inhibit HIV infection by blocking those receptors. Removal of chemokine receptors from the cell surface using polymorphisms or other means confers some levels of immunity against HIV infection. Up to now, very limited success has been obtained using ligand therapies so we explored potential avenues to regulate chemokine receptor expression at the plasma membrane. We identified a molecular chaperone, DRiP78, that interacts with both CXCR4 and CCR5, but not the heterodimer formed by these receptors. We further characterized the effects of DRiP78 on CCR5 function. We show that the molecular chaperone inhibits CCR5 localization to the plasma membrane. We identified the interaction region on the receptor, the F(x)6LL motif, and show that upon mutation of this motif the chaperone cannot interact with the receptor. We also show that DRiP78 is involved in the assembly of CCR5 chemokine signaling complex as a homodimer, as well as with the Gαi protein. Finally, modulation of DRiP78 levels will affect receptor functions, such as cell migration in cells that endogenously express CCR5. Our results demonstrate that modulation of the functions of a chaperone can affect signal transduction at the cell surface.

  12. Synchronization patterns: from network motifs to hierarchical networks

    Science.gov (United States)

    Krishnagopal, Sanjukta; Lehnert, Judith; Poel, Winnie; Zakharova, Anna; Schöll, Eckehard

    2017-03-01

    We investigate complex synchronization patterns such as cluster synchronization and partial amplitude death in networks of coupled Stuart-Landau oscillators with fractal connectivities. The study of fractal or self-similar topology is motivated by the network of neurons in the brain. This fractal property is well represented in hierarchical networks, for which we present three different models. In addition, we introduce an analytical eigensolution method and provide a comprehensive picture of the interplay of network topology and the corresponding network dynamics, thus allowing us to predict the dynamics of arbitrarily large hierarchical networks simply by analysing small network motifs. We also show that oscillation death can be induced in these networks, even if the coupling is symmetric, contrary to previous understanding of oscillation death. Our results show that there is a direct correlation between topology and dynamics: hierarchical networks exhibit the corresponding hierarchical dynamics. This helps bridge the gap between mesoscale motifs and macroscopic networks. This article is part of the themed issue 'Horizons of cybernetical physics'.

  13. Graph animals, subgraph sampling and motif search in large networks

    CERN Document Server

    Baskerville, Kim; Paczuski, Maya

    2007-01-01

    We generalize a sampling algorithm for lattice animals (connected clusters on a regular lattice) to a Monte Carlo algorithm for `graph animals', i.e. connected subgraphs in arbitrary networks. As with the algorithm in [N. Kashtan et al., Bioinformatics 20, 1746 (2004)], it provides a weighted sample, but the computation of the weights is much faster (linear in the size of subgraphs, instead of super-exponential). This allows subgraphs with up to ten or more nodes to be sampled with very high statistics, from arbitrarily large networks. Using this together with a heuristic algorithm for rapidly classifying isomorphic graphs, we present results for two protein interaction networks obtained using the TAP high throughput method: one of Escherichia coli with 230 nodes and 695 links, and one for yeast (Saccharomyces cerevisiae) with roughly ten times more nodes and links. We find in both cases that most connected subgraphs are strong motifs (Z-scores >10) or anti-motifs (Z-scores <-10) when the null model is the...

  14. Prevalent RNA recognition motif duplication in the human genome.

    Science.gov (United States)

    Tsai, Yihsuan S; Gomez, Shawn M; Wang, Zefeng

    2014-05-01

    The sequence-specific recognition of RNA by proteins is mediated through various RNA binding domains, with the RNA recognition motif (RRM) being the most frequent and present in >50% of RNA-binding proteins (RBPs). Many RBPs contain multiple RRMs, and it is unclear how each RRM contributes to the binding specificity of the entire protein. We found that RRMs within the same RBP (i.e., sibling RRMs) tend to have significantly higher similarity than expected by chance. Sibling RRM pairs from RBPs shared by multiple species tend to have lower similarity than those found only in a single species, suggesting that multiple RRMs within the same protein might arise from domain duplication followed by divergence through random mutations. This finding is exemplified by a recent RRM domain duplication in DAZ proteins and an ancient duplication in PABP proteins. Additionally, we found that different similarities between sibling RRMs are associated with distinct functions of an RBP and that the RBPs tend to contain repetitive sequences with low complexity. Taken together, this study suggests that the number of RBPs with multiple RRMs has expanded in mammals and that the multiple sibling RRMs may recognize similar target motifs in a cooperative manner.

  15. The discodermolide hairpin structure flows from conformationally stable modular motifs.

    Science.gov (United States)

    Jogalekar, Ashutosh S; Kriel, Frederik H; Shi, Qi; Cornett, Ben; Cicero, Daniel; Snyder, James P

    2010-01-14

    (+)-Discodermolide (DDM), a polyketide macrolide from marine sponge, is a potent microtubule assembly promoter. Reported solid-state, solution, and protein-bound DDM conformations reveal the unusual result that a common hairpin conformational motif exists in all three microenvironments. No other flexible microtubule binding agent exhibits such constancy of conformation. In the present study, we combine force-field conformational searches with NMR deconvolution in different solvents to compare DDM conformers with those observed in other environments. While several conformational families are perceived, the hairpin form dominates. The stability of this motif is dictated primarily by steric factors arising from repeated modular segments in DDM composed of the C(Me)-CHX-C(Me) fragment. Furthermore, docking protocols were utilized to probe the DDM binding mode in beta-tubulin. A previously suggested pose is substantiated (Pose-1), while an alternative (Pose-2) has been identified. SAR analysis for DDM analogues differentiates the two poses and suggests that Pose-2 is better able to accommodate the biodata.

  16. The Origin of Motif Families in Food Webs

    CERN Document Server

    Klaise, Janis

    2016-01-01

    Food webs have been found to exhibit remarkable motif profiles, patterns in the relative prevalences of all possible three-species sub-graphs, and this has been related to ecosystem properties such as stability and robustness. Analysing 46 food webs of various kinds, we find that most food webs fall into one of two distinct motif families. The separation between the families is well predicted by a global measure of hierarchical order in directed networks - trophic coherence. We find that trophic coherence is also a good predictor for the extent of omnivory, defined as the tendency of species to feed on multiple trophic levels. We compare our results to a network assembly model that admits tunable trophic coherence via a single free parameter. The model is able to generate food webs in either of the two families by varying this parameter, and correctly classifies almost all the food webs in our database. This establishes a link between global order and local preying patterns in food webs.

  17. Phosphotyrosine Substrate Sequence Motifs for Dual Specificity Phosphatases.

    Directory of Open Access Journals (Sweden)

    Bryan M Zhao

    Full Text Available Protein tyrosine phosphatases dephosphorylate tyrosine residues of proteins, whereas, dual specificity phosphatases (DUSPs are a subgroup of protein tyrosine phosphatases that dephosphorylate not only Tyr(P residue, but also the Ser(P and Thr(P residues of proteins. The DUSPs are linked to the regulation of many cellular functions and signaling pathways. Though many cellular targets of DUSPs are known, the relationship between catalytic activity and substrate specificity is poorly defined. We investigated the interactions of peptide substrates with select DUSPs of four types: MAP kinases (DUSP1 and DUSP7, atypical (DUSP3, DUSP14, DUSP22 and DUSP27, viral (variola VH1, and Cdc25 (A-C. Phosphatase recognition sites were experimentally determined by measuring dephosphorylation of 6,218 microarrayed Tyr(P peptides representing confirmed and theoretical phosphorylation motifs from the cellular proteome. A broad continuum of dephosphorylation was observed across the microarrayed peptide substrates for all phosphatases, suggesting a complex relationship between substrate sequence recognition and optimal activity. Further analysis of peptide dephosphorylation by hierarchical clustering indicated that DUSPs could be organized by substrate sequence motifs, and peptide-specificities by phylogenetic relationships among the catalytic domains. The most highly dephosphorylated peptides represented proteins from 29 cell-signaling pathways, greatly expanding the list of potential targets of DUSPs. These newly identified DUSP substrates will be important for examining structure-activity relationships with physiologically relevant targets.

  18. Structure-Function Similarities between a Plant Receptor-like Kinase and the Human Interleukin-1 Receptor-associated Kinase-4*

    OpenAIRE

    2011-01-01

    Phylogenetic analysis has previously shown that plant receptor-like kinases (RLKs) are monophyletic with respect to the kinase domain and share an evolutionary origin with the animal interleukin-1 receptor-associated kinase/Pelle-soluble kinases. The lysin motif domain-containing receptor-like kinase-3 (LYK3) of the legume Medicago truncatula shows 33% amino acid sequence identity with human IRAK-4 over the kinase domain. Using the structure of this animal kinase as a template, homology model...

  19. Effectiveness of Diffusion Barrier Coatings for Mo-Re Embedded in C/SiC and C/C

    Science.gov (United States)

    Glass, David E.; Shenoy, Ravi N.; Wang, Zeng-Mei; Halbig, Michael C.

    2001-01-01

    Advanced high-temperature cooling applications may often require the elevated-temperature capability of carbon/silicon carbide or carbon/carbon composites in combination with the hermetic capability of metallic tubes. In this paper, the effects of C/SiC and C/C on tubes fabricated from several different refractory metals were evaluated. Though Mo, Nb, and Re were evaluated in the present study, the primary effort was directed toward two alloys of Mo-Re, namely, arc cast Mo-41Re and powder metallurgy Mo-47.5Re. Samples of these refractory metals were subjected to either the PyC/SiC deposition or embedding in C/C. MoSi2(Ge), R512E, and TiB2 coatings were included on several of the samples as potential diffusion barriers. The effects of the processing and thermal exposure on the samples were evaluated by conducting burst tests, microhardness surveys, and scanning electron microscopic examination (using either secondary electron or back scattered electron imaging and energy dispersive spectroscopy). The results showed that a layer of brittle Mo-carbide formed on the substrates of both the uncoated Mo-41Re and the uncoated Mo-47.5Re, subsequent to the C/C or the PyC/SiC processing. Both the R512E and the MoSi2(Ge) coatings were effective in preventing not only the diffusion of C into the Mo-Re substrate, but also the formation of the Mo-carbides. However, none of the coatings were effective at preventing both C and Si diffusion without some degradation of the substrate.

  20. The endocytosis and signaling of the γδ T cell coreceptor WC1 are regulated by a dileucine motif.

    Science.gov (United States)

    Hsu, Haoting; Baldwin, Cynthia L; Telfer, Janice C

    2015-03-01

    WC1 proteins, which are specifically expressed by bovine γδ T cells from a gene array containing 13 members, are part of the scavenger receptor cysteine-rich family. WC1 cytoplasmic domains contains multiple tyrosines, one of which is required to be phosphorylated for TCR coreceptor activity, and a dileucine endocytosis motif. Like the TCR coreceptor CD4, WC1 is endocytosed in response to PMA. Because WC1 endocytosis may play a role in the activation of γδ T cells, we examined WC1 endocytosis in the adherent cell 293T and Jurkat T cell lines using a fusion protein of extracellular CD4 and the transmembrane and cytoplasmic domain of WC1. Individual mutation of the two leucine residues of the endocytic dileucine motif in the WC1 cytoplasmic domain significantly reduced PMA-induced endocytosis in both cell types and enhanced IL-2 production stimulated by cocross-linking of CD3/TCR and CD4/WC1 in Jurkat cells, suggesting that the sustained membrane coligation of CD3/TCR with WC1 caused by a decrease in endocytosis increases T cell activation. Mutation of two serines upstream of the endocytic dileucine motif affected endocytosis only in adherent 293T cells. Although the two upstream serines were not required for WC1 endocytosis in Jurkat cells, the pan-protein kinase C inhibitor Gö6983 blocked endocytosis of CD4/WC1, and mutation of the upstream serines in WC1 inhibited IL-2 production stimulated by cocross-linking of CD3/TCR and CD4/WC1. These studies provide insights into the signaling of WC1 gene arrays that are present in most mammals and play critical roles in γδ T cell responses to bacterial pathogens.

  1. 基于C & C08-Q的UniCenter2013中间层的设计与实现%Design and implementation of UniCenter2013 intermediate layer based on C & C08-Q

    Institute of Scientific and Technical Information of China (English)

    李淑玲

    2014-01-01

    基于C&C08-Q的UniCenter2013呼叫中心项目,将强大的互联网同固定电话网统一起来,为客户提供了一个功能完备且全天候服务的客户中心。中间层是整个呼叫中心系统构建中的基础模块,本文为用户提供了一个完善的数据库访问解决方案,从而增强了系统的扩展性和可维护性。%The UniCenter2013 Call Center project is based on C&C08-Q,integrating powerful Internet and fixed telephone network,providing a feature complete and all whether service customer center.The intermediate layer is the basic module in the whole call center system, this chapter providing a perfect solution for accessing the database,so enhanced the system extensibility and maintainability.

  2. Method 446.0: In Vitro Determination of Chlorophylls a, b, c + c and Pheopigments in 1 2Marine And Freshwater Algae by Visible Spectrophotometry

    Science.gov (United States)

    This method provides a procedure for determination of chlorophylls a (chl a), b (chl b), c + c 1 2 (chl c + c ) and pheopigments of chlorophyll a (pheo a) 1 2 found in marine and freshwater phytoplankton. Chlorophyllide a is determined as chl a. Visible wavelength spectrophotomet...

  3. The Academic and Remedial Placement of Students Entering B. C. C. in September 1975 by Curriculum Group. Research Report BCC-9-75.

    Science.gov (United States)

    Bronx Community Coll., NY.

    This report describes the Bronx Community College (B.C.C.) freshmen class entering in September 1975, in terms of high school grade average and scores on reading-English and mathematics placement tests. As of the fall of 1974, B.C.C. enrolled a markedly higher proportion of students with high school averages below 70 percent than any other college…

  4. Dielectron Production in C+C Collisions at 1 GeV/u and the Solution to the DLS Puzzle

    CERN Document Server

    Pachmayer, Y C; Agodi, C; Balanda, A; Bellia, G; Belver, D; Belyaev, A; Blanco, A; Bhömer, M; Boyard, J L; Braun-Munzinger, P; Cabanelas, P; Castro, oE; Chernenko, S; Christ, T; Destefanis, M; Daz, J; Dohrmann, F; Dybczak, A; Eberl, T; Fabbietti, L; Fateev, O; Finocchiaro, P; Fonte, Paulo J R; Friese, J; Fröhlich, I; Galatyuk, T; Garzn, J A; Gernhuser, R; Gil, A; Gilardi, C; Golubeva, M; Gonzalez-Diaz, D; Grosse, E; Guber, F; Heilmann, M; Hennino, T; Holzmann, R; Ierusalimov, A; Iori, I; Ivashkin, A; Jurkovic, M; Kmpfer, B; Kanaki, K; Karavicheva, T; Kirschner, D; König, I; König, W; Kolb, B W; Kotte, R; Kozuch, A; Krsa, A; Krizek, F; Krücken, R; Kühn, W; Kugler, A; Kurepin, A; Lamas-Valverde, J; Lang, S; Lange, J S; Lapidus, K; Lopes, L; Lorenz, M; Maier, L; Mangiarotti, A; Marn, J; Markert, J; Metag, V; Michalska, B; Michel, J; Mishra, D; Moriniere, E; Mousa, J; Müntz, C; Naumann, Lutz; Novotny, R; Otwinowski, J; Palka, M; Parpottas, Y; Pechenov, V; Pechenova, O; Prez Cavalcanti, T; Pietraszko, J; Przygoda, W; Ramstein, B; Reshetin, A; Roy-Stephan, M; Rustamov, A; Sadovskii, A; Sailer, B; Salabura, P; Schmah, A; Simon, R; Sobolev, Yu G; Spataro, S; Spruck, B; Strbele, H; Stroth, J; Sturm, C; Sudol, M; Tarantola, A; Teilab, K; Tlustý, P; Traxler, M; Trebacz, R; Tsertos, H; Veretenkin, I; Wagner, V; Wen, H; Wisniowski, M; Wojcik, T; Wüstenfeld, J; Yurevich, S; Zanevsky, Y; Zhou, P; Zumbruch, P

    2008-01-01

    The production of e+e- pairs in C+C collisions at 1 GeV/u was investigated with the HADES experiment at GSI, Darmstadt. In the invariant-mass region $ 0.15\\: GeV/c^{2} \\leq M_{ee} \\leq 0.5\\: GeV/c^{2}$ the measured pair yield shows a strong excess above the contribution expected from hadron decays after freeze-out. The data are in good agreement with the results of the former DLS experiment for the same system and energy.

  5. EFFECTS OF HIGH TEMPERATURE PRETREATMENTS ON HIGH TEMPERATURE FRACTURE BEHAVIOR OF SiC-C/SiC

    Institute of Scientific and Technical Information of China (English)

    X.G. Luan; L.F. Cheng; S.R. Qiao; J. Zhang

    2004-01-01

    The samples made from a SiC-C/SiC composite were pretreated in Ar under creep,fatigue, creep and fatigue interaction, as well as in dry oxygen and wet oxygen under fatigue at 1300℃ for 15 hours. The fracture behaviors of the pretreated samples were investigated at 1300℃. The loading-strain curves and the microstructures of the sample were compared with each other. The various of high temperature tensile behaviors was attributed to the different microstructures resulted from different high temperature pretreatments.

  6. Numerical modelling of micro-machining of f.c.c. single crystal: Influence of strain gradients

    KAUST Repository

    Demiral, Murat

    2014-11-01

    A micro-machining process becomes increasingly important with the continuous miniaturization of components used in various fields from military to civilian applications. To characterise underlying micromechanics, a 3D finite-element model of orthogonal micro-machining of f.c.c. single crystal copper was developed. The model was implemented in a commercial software ABAQUS/Explicit employing a user-defined subroutine VUMAT. Strain-gradient crystal-plasticity and conventional crystal-plasticity theories were used to demonstrate the influence of pre-existing and evolved strain gradients on the cutting process for different combinations of crystal orientations and cutting directions. Crown Copyright © 2014.

  7. Bonding and Integration of C-C Composite to Cu-Clad-Molybdenum for Thermal Management Applications

    Science.gov (United States)

    Asthana, R.; Singh, M.; Shpargel, T.P.

    2008-01-01

    Two- and three-dimensional carbon-carbon composites with either resin-derived matrix or CVI matrix were joined to Cu-clad-Mo using active Ag-Cu braze alloys for thermal management applications. The joint microstructure and composition were examined using Field-Emission Scanning Electron Microscopy and Energy-Dispersive Spectroscopy, and the joint hardness was characterized using the Knoop microhardness testing. Observations on the infiltration of the composite with molten braze, dissolution of metal substrate, and solute segregation at the C-C surface have been discussed. The thermal response of the integrated assembly is also briefly discussed.

  8. Palladium complexes containing diphosphine and sulfonated phosphine ligands for c-c bond forming reactions. catalytic and mechanistic studies

    OpenAIRE

    García Suárez, Eduardo José

    2007-01-01

    El uso de compuestos de paladio(II) para catalizar reacciones de copolimerización de monóxido de carbono y olefinas así como otros tipos de reacciones de formación de enlaces C-C muestra un creciente interés, prueba de ello es el importante numero de publicaciones realizadas en estos últimos años.En catálisis una de las mayores causas de baja productividad es la degradación del catalizador a especies menos activas. Por este motivo se dedican constantemente esfuerzos al diseño de ligandos capa...

  9. Sequence Length Limits for Controlling False Positives in Discovering Nucleotide Sequence Motifs

    Institute of Scientific and Technical Information of China (English)

    CHEN Lei; QiAN Zi-liang

    2008-01-01

    In the study of motif discovery, especially the transcription factor DNA binding sites discovery, a too long input sequence would return non-informative motifs rather than those biological functional motifs. This paper gave theoretical analyses and computational experiments to suggest the length limits of the input sequence. When the sequence length exceeds a certain critical point, the probability of discovering the motif decreases sharply. The work not only gave an explanation on the unsatisfying results of the existed motif discovery problems that the input sequence length might be too long and exceed the point, but also provided an estimation of input sequence length we should accept to get more meaningful and reliable results in motif discovery.

  10. Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

    Science.gov (United States)

    Sharov, Alexei A.; Ko, Minoru S.H.

    2009-01-01

    We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cells based on published chromatin immunoprecipitation sequencing data. Furthermore, CisFinder successfully identified alternative binding motifs of TFs (e.g. POU5F1, ESRRB, and CTCF) and motifs for known and unknown co-factors of genes associated with the pluripotent state of ES cells. CisFinder also showed robust performance in the identification of motifs that were only slightly enriched in a set of DNA sequences. PMID:19740934

  11. The first intracellular loop of GLUT4 contains a retention motif.

    Science.gov (United States)

    Talantikite, Maya; Berenguer, Marion; Gonzalez, Teresa; Alessi, Marie Christine; Poggi, Marjorie; Peiretti, Franck; Govers, Roland

    2016-06-01

    Glucose transporter GLUT4 (also known as SLC2A4) plays a major role in glucose homeostasis and is efficiently retained intracellularly in adipocytes and myocytes. To simplify the analysis of its retention, here, various intracellular GLUT4 domains were fused individually to reporter molecules. Of the four short cytoplasmic loops of GLUT4, only the first nine-residue-long loop conferred intracellular retention of truncated forms of the transferrin receptor and CD4 in adipocytes. In contrast, the same loop of GLUT1 was without effect. The reporter molecules to which the first loop of GLUT4 was fused localized, unlike GLUT4, to the trans-Golgi network (TGN), possibly explaining why these molecules did not respond to insulin. The retention induced by the GLUT4 loop was specific to adipocytes as it did not induce retention in preadipocytes. Of the SQWLGRKRA sequence that constitutes this loop, mutation of either the tryptophan or lysine residue abrogated reporter retention. Mutation of these residues individually into alanine residues in the full-length GLUT4 molecule resulted in a decreased retention for GLUT4-W105A. We conclude that the first intracellular loop of GLUT4 contains the retention motif WLGRK, in which W105 plays a prominent role.

  12. Effects of chemokine (C–C motif) ligand 1 on microglial function

    Energy Technology Data Exchange (ETDEWEB)

    Akimoto, Nozomi [Laboratory of Pathophysiology, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan); Ifuku, Masataka [Laboratory of Integrative Physiology, Graduate School of Medicine, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan); Mori, Yuki [Laboratory of Pathophysiology, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan); Noda, Mami, E-mail: noda@phar.kyushu-u.ac.jp [Laboratory of Pathophysiology, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan)

    2013-07-05

    Highlights: •CCR8, a specific receptor for CCL-1, was expressed on primary cultured microglia. •Expression of CCR-8 in microglia was upregulated in the presence of CCL-1. •CCL-1 increased motility, proliferation and phagocytosis of cultured microglia. •CCL-1promoted BDNF and IL-6 mRNA, and the release of NO from microglia. •CCL-1 activates microglia and may contribute to the development of neuropathic pain. -- Abstract: Microglia, which constitute the resident macrophages of the central nervous system (CNS), are generally considered as the primary immune cells in the brain and spinal cord. Microglial cells respond to various factors which are produced following nerve injury of multiple aetiologies and contribute to the development of neuronal disease. Chemokine (C–C motif) ligand 1 (CCL-1), a well-characterized chemokine secreted by activated T cells, has been shown to play an important role in neuropathic pain induced by nerve injury and is also produced in various cell types in the CNS, especially in dorsal root ganglia (DRG). However, the role of CCL-1 in the CNS and the effects on microglia remains unclear. Here we showed the multiple effects of CCL-1 on microglia. We first showed that CCR-8, a specific receptor for CCL-1, was expressed on primary cultured microglia, as well as on astrocytes and neurons, and was upregulated in the presence of CCL-1. CCL-1 at concentration of 1 ng/ml induced chemotaxis, increased motility at a higher concentration (100 ng/ml), and increased proliferation and phagocytosis of cultured microglia. CCL-1 also activated microglia morphologically, promoted mRNA levels for brain-derived neurotrophic factor (BDNF) and IL-6, and increased the release of nitrite from microglia. These indicate that CCL-1 has a role as a mediator in neuron-glia interaction, which may contribute to the development of neurological diseases, especially in neuropathic pain.

  13. The value of position-specific priors in motif discovery using MEME

    Directory of Open Access Journals (Sweden)

    Whitington Tom

    2010-04-01

    Full Text Available Abstract Background Position-specific priors have been shown to be a flexible and elegant way to extend the power of Gibbs sampler-based motif discovery algorithms. Information of many types–including sequence conservation, nucleosome positioning, and negative examples–can be converted into a prior over the location of motif sites, which then guides the sequence motif discovery algorithm. This approach has been shown to confer many of the benefits of conservation-based and discriminative motif discovery approaches on Gibbs sampler-based motif discovery methods, but has not previously been studied with methods based on expectation maximization (EM. Results We extend the popular EM-based MEME algorithm to utilize position-specific priors and demonstrate their effectiveness for discovering transcription factor (TF motifs in yeast and mouse DNA sequences. Utilizing a discriminative, conservation-based prior dramatically improves MEME's ability to discover motifs in 156 yeast TF ChIP-chip datasets, more than doubling the number of datasets where it finds the correct motif. On these datasets, MEME using the prior has a higher success rate than eight other conservation-based motif discovery approaches. We also show that the same type of prior improves the accuracy of motifs discovered by MEME in mouse TF ChIP-seq data, and that the motifs tend to be of slightly higher quality those found by a Gibbs sampling algorithm using the same prior. Conclusions We conclude that using position-specific priors can substantially increase the power of EM-based motif discovery algorithms such as MEME algorithm.

  14. Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

    OpenAIRE

    Sharov, Alexei A; Minoru S.H. Ko

    2009-01-01

    We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cel...

  15. NestedMICA as an ab initio protein motif discovery tool

    Directory of Open Access Journals (Sweden)

    Down Thomas A

    2008-01-01

    Full Text Available Abstract Background Discovering overrepresented patterns in amino acid sequences is an important step in protein functional element identification. We adapted and extended NestedMICA, an ab initio motif finder originally developed for finding transcription binding site motifs, to find short protein signals, and compared its performance with another popular protein motif finder, MEME. NestedMICA, an open source protein motif discovery tool written in Java, is driven by a Monte Carlo technique called Nested Sampling. It uses multi-class sequence background models to represent different "uninteresting" parts of sequences that do not contain motifs of interest. In order to assess NestedMICA as a protein motif finder, we have tested it on synthetic datasets produced by spiking instances of known motifs into a randomly selected set of protein sequences. NestedMICA was also tested using a biologically-authentic test set, where we evaluated its performance with respect to varying sequence length. Results Generally NestedMICA recovered most of the short (3–9 amino acid long test protein motifs spiked into a test set of sequences at different frequencies. We showed that it can be used to find multiple motifs at the same time, too. In all the assessment experiments we carried out, its overall motif discovery performance was better than that of MEME. Conclusion NestedMICA proved itself to be a robust and sensitive ab initio protein motif finder, even for relatively short motifs that exist in only a small fraction of sequences. Availability NestedMICA is available under the Lesser GPL open-source license from: http://www.sanger.ac.uk/Software/analysis/nmica/

  16. N-terminal tetrapeptide T/SPLH motifs contribute to multimodal activation of human TRPA1 channel

    Science.gov (United States)

    Hynkova, Anna; Marsakova, Lenka; Vaskova, Jana; Vlachova, Viktorie

    2016-06-01

    Human transient receptor potential ankyrin channel 1 (TRPA1) is a polymodal sensor implicated in pain, inflammation and itching. An important locus for TRPA1 regulation is the cytoplasmic N-terminal domain, through which various exogenous electrophilic compounds such as allyl-isothiocyanate from mustard oil or cinnamaldehyde from cinnamon activate primary afferent nociceptors. This major region is comprised of a tandem set of 17 ankyrin repeats (AR1-AR17), five of them contain a strictly conserved T/SPLH tetrapeptide motif, a hallmark of an important and evolutionarily conserved contribution to conformational stability. Here, we characterize the functional consequences of putatively stabilizing and destabilizing mutations in these important structural units and identify AR2, AR6, and AR11-13 to be distinctly involved in the allosteric activation of TRPA1 by chemical irritants, cytoplasmic calcium, and membrane voltage. Considering the potential involvement of the T/SP motifs as putative phosphorylation sites, we also show that proline-directed Ser/Thr kinase CDK5 modulates the activity of TRPA1, and that T673 outside the AR-domain is its only possible target. Our data suggest that the most strictly conserved N-terminal ARs define the energetics of the TRPA1 channel gate and contribute to chemical-, calcium- and voltage-dependence.

  17. A motif extraction algorithm based on hashing and modulo-4 arithmetic.

    Science.gov (United States)

    Sheng, Huitao; Mehrotra, Kishan; Mohan, Chilukuri; Raina, Ramesh

    2008-01-01

    We develop an algorithm to identify cis-elements in promoter regions of coregulated genes. This algorithm searches for subsequences of desired length whose frequency of occurrence is relatively high, while accounting for slightly perturbed variants using hash table and modulo arithmetic. Motifs are evaluated using profile matrices and higher-order Markov background model. Simulation results show that our algorithm discovers more motifs present in the test sequences, when compared with two well-known motif-discovery tools (MDScan and AlignACE). The algorithm produces very promising results on real data set; the output of the algorithm contained many known motifs.

  18. Mapping network motif tunability and robustness in the design of synthetic signaling circuits.

    Directory of Open Access Journals (Sweden)

    Sergio Iadevaia

    Full Text Available Cellular networks are highly dynamic in their function, yet evolutionarily conserved in their core network motifs or topologies. Understanding functional tunability and robustness of network motifs to small perturbations in function and structure is vital to our ability to synthesize controllable circuits. In establishing core sets of network motifs, we selected topologies that are overrepresented in mammalian networks, including the linear, feedback, feed-forward, and bifan circuits. Static and dynamic tunability of network motifs were defined as the motif ability to respectively attain steady-state or transient outputs in response to pre-defined input stimuli. Detailed computational analysis suggested that static tunability is insensitive to the circuit topology, since all of the motifs displayed similar ability to attain predefined steady-state outputs in response to constant inputs. Dynamic tunability, in contrast, was tightly dependent on circuit topology, with some motifs performing superiorly in achieving observed time-course outputs. Finally, we mapped dynamic tunability onto motif topologies to determine robustness of motif structures to changes in topology and identify design principles for the rational assembly of robust synthetic networks.

  19. Shear and Flexural Behaviour of R.C.C. Beam With Circular Opening Strengthened By CFRP Sheets

    Directory of Open Access Journals (Sweden)

    VinayChakrasali

    2015-04-01

    Full Text Available This paper explores the behavior of R.C.C. beam with circular opening strengthened by CFRP sheets. In this experimental work five beams were casted, one beam without opening (i.e. solid beam and one with circular post opening and considered as control beams. The remaining three beams were externally strengthened by Carbon fiber reinforced polymer (CFRP sheets with different strengthening schemes i.e. around the opening, inside the opening. These beams were simply supported and tested less than two points loading in the loading frame. The behaviors of such beams were studied in terms of load carrying capacity, load-deflection behavior and cracking patterns. From the test results it is concluded that the ultimate load carrying capacity of the R.C.C. beam strengthened with CFRP sheets increased in the range of 13.01% to 55.32%. Among all the strengthening schemes, the strengthening with CFRP around and inside the opening was found very effective in improving the ultimate load carrying capacity of beam.

  20. Pd loaded amphiphilic COF as catalyst for multi-fold Heck reactions, C-C couplings and CO oxidation.

    Science.gov (United States)

    Mullangi, Dinesh; Nandi, Shyamapada; Shalini, Sorout; Sreedhala, Sheshadri; Vinod, Chathakudath P; Vaidhyanathan, Ramanathan

    2015-06-09

    COFs represent a class of polymers with designable crystalline structures capable of interacting with active metal nanoparticles to form excellent heterogeneous catalysts. Many valuable ligands/monomers employed in making coordination/organic polymers are prepared via Heck and C-C couplings. Here, we report an amphiphilic triazine COF and the facile single-step loading of Pd(0) nanoparticles into it. An 18-20% nano-Pd loading gives highly active composite working in open air at low concentrations (Conc. Pd(0) couplings and C-C couplings using 'non-boronic acid' substrates, and exhibits good recyclability with no sign of catalyst leaching. As an oxidation catalyst, it shows 100% conversion of CO to CO2 at 150 °C with no loss of activity with time and between cycles. Both vapor sorptions and contact angle measurements confirm the amphiphilic character of the COF. DFT-TB studies showed the presence of Pd-triazine and Pd-Schiff bond interactions as being favorable.

  1. NIBLES - an HI census of stellar mass selected SDSS galaxies: I. The Nan\\c{c}ay HI survey

    CERN Document Server

    van Driel, W; Schneider, S; Lehnert, M D; Minchin, R; Blyth, S-L; Chemin, L; Hallet, N; Joseph, T; Kotze, P; Kraan-Korteweg, R C; Olofsson, A O H; Ramatsoku, M

    2016-01-01

    To investigate galaxy properties as a function of their total stellar mass, we obtained 21cm HI line observations at the 100-m class Nan\\c{c}ay Radio Telescope of 2839 galaxies from the Sloan Digital Sky Survey (SDSS) in the Local Volume (900c{c}ay Interstellar Baryons Legacy Extragalactic Survey (NIBLES) sample. They were selected evenly over their entire range of absolute SDSS z-band magnitudes (-13.5 to -24 mag), which were used as a proxy for their stellar masses. Here, a first, global presentation of the observations and basic results is given, their further analysis will be presented in other papers in this series. The galaxies were selected based on their properties, as listed in SDSS DR5. Comparing this photometry to their total HI masses, we noted that, for a few percent, the SDSS magnitudes appeared severely misunderestimated, as confirmed by our re-measurements for selected objects. Although using the later DR9 results eliminated this problem in most cases, 38...

  2. Preparation and characteristics of C/C composite brake disc by multi-cylindrical chemical vapor deposition processes

    Institute of Scientific and Technical Information of China (English)

    YUAN Yi-dong; ZHANG Fu-kuan; ZHOU Wan-cheng

    2005-01-01

    The C/C composite brake discs were prepared by tri-cylindrical chemical vapor deposition (CVD) process. The optimum processing parameters were as follows: deposition temperature was 830-930 ℃, the gas-flow rates of N2 and propylene were 4.8-5.2 m3/h and 5.8-6.2 m3/h, respectively, the furnace pressure was 4.5-5.5 kPa and the deposition time was 200 h.The effects of processing parameters on the densified rates, thermal-physical property and mechanical performance of C/C composite brake discs were studied. The results show that density, heat conductivity, bend strength and abrasion ratio of the multi-cylindrica brake discs are 1.02-1.78 g/cm3, 31 W/(m·K), 114 MPa and 7 μm/s, respectively, which are approximately similar to those of the single-cylindrical ones. The gas flow rate has no relation to the number of the cylinder and furnace loading. The utilization ratio of carbon can be improved by multi-cylinder CVD process without changing the characteristics of brake disc.

  3. First observation of the isospin violating decay $J/\\psi\\rightarrow \\Lambda\\bar{\\Sigma}^{0}+c.c.$

    CERN Document Server

    Ablikim, M; Ambrose, D J; An, F F; An, Q; An, Z H; Bai, J Z; Ban, Y; Becker, J; Berger, N; Bertani, M; Bian, J M; Boger, E; Bondarenko, O; Boyko, I; Briere, R A; Bytev, V; Cai, X; Cakir, O; Calcaterra, A; Cao, G F; Cetin, S A; Chang, J F; Chelkov, G; Chen, G; Chen, H S; Chen, J C; Chen, M L; Chen, S J; Chen, Y; Chen, Y B; Cheng, H P; Chu, Y P; Cronin-Hennessy, D; Dai, H L; Dai, J P; Dedovich, D; Deng, Z Y; Denig, A; Denysenko, I; Destefanis, M; Ding, W M; Ding, Y; Dong, L Y; Dong, M Y; Du, S X; Fang, J; Fang, S S; Fava, L; Feldbauer, F; Feng, C Q; Ferroli, R B; Fu, C D; Fu, J L; Gao, Y; Geng, C; Goetzen, K; Gong, W X; Gradl, W; Greco, M; Gu, M H; Gu, Y T; Guan, Y H; Guo, A Q; Guo, L B; Guo, Y P; Han, Y L; Hao, X Q; Harris, F A; He, K L; He, M; He, Z Y; Held, T; Heng, Y K; Hou, Z L; Hu, H M; Hu, J F; Hu, T; Huang, B; Huang, G M; Huang, J S; Huang, X T; Huang, Y P; Hussain, T; Ji, C S; Ji, Q; Ji, X B; Ji, X L; Jia, L K; Jiang, L L; Jiang, X S; Jiao, J B; Jiao, Z; Jin, D P; Jin, S; Jing, F F; Kalantar-Nayestanaki, N; Kavatsyuk, M; Kuehn, W; Lai, W; Lange, J S; Li, C H; Li, Cheng; Li, Cui; Li, D M; Li, F; Li, G; Li, H B; Li, J C; Li, K; Li, Lei; Li, N B; Li, Q J; Li, S L; Li, W D; Li, W G; Li, X L; Li, X N; Li, X Q; Li, X R; Li, Z B; Liang, H; Liang, Y F; Liang, Y T; Liao, G R; Liao, X T; Liu, B J; Liu, C L; Liu, C X; Liu, C Y; Liu, F H; Liu, Fang; Liu, Feng; Liu, H; Liu, H B; Liu, H H; Liu, H M; Liu, H W; Liu, J P; Liu, K Y; Liu, Kai; Liu, Kun; Liu, P L; Liu, S B; Liu, X; Liu, X H; Liu, Y; Liu, Y B; Liu, Z A; Liu, Zhiqiang; Liu, Zhiqing; Loehner, H; Lu, G R; Lu, H J; Lu, J G; Lu, Q W; Lu, X R; Lu, Y P; Luo, C L; Luo, M X; Luo, T; Luo, X L; Lv, M; Ma, C L; Ma, F C; Ma, H L; Ma, Q M; Ma, S; Ma, T; Ma, X Y; Ma, Y; Maas, F E; Maggiora, M; Malik, Q A; Mao, H; Mao, Y J; Mao, Z P; Messchendorp, J G; Min, J; Min, T J; Mitchell, R E; Mo, X H; Morales, C Morales; Motzko, C; Muchnoi, N Yu; Muramatsu, H; Nefedov, Y; Nicholson, C; Nikolaev, I B; Ning, Z; Olsen, S L; Ouyang, Q; Pacetti, S; Park, J W; Pelizaeus, M; Peng, H P; Peters, K; Ping, J L; Ping, R G; Poling, R; Prencipe, E; Qi, M; Qian, S; Qiao, C F; Qin, X S; Qin, Y; Qin, Z H; Qiu, J F; Rashid, K H; Rong, G; Ruan, X D; Sarantsev, A; Schaefer, B D; Schulze, J; Shao, M; Shen, C P; Shen, X Y; Sheng, H Y; Shepherd, M R; Song, X Y; Spataro, S; Spruck, B; Sun, D H; Sun, G X; Sun, J F; Sun, S S; Sun, X D; Sun, Y J; Sun, Y Z; Sun, Z J; Sun, Z T; Tang, C J; Tang, X; Tapan, X F Tang I; Thorndike, E H; Tian, H L; Toth, D; Ullrich, M; Varner, G S; Wang, B; Wang, B Q; Wang, K; Wang, L L; Wang, L S; Wang, M; Wang, P; Wang, P L; Wang, Q; Wang, Q J; Wang, S G; Wang, X L; Wang, Y D; Wang, Y F; Wang, Y Q; Wang, Z; Wang, Z G; Wang, Z Y; Wei, D H; Weidenkaff, P; Wen, Q G; Wen, S P; Werner, M; Wiedner, U; Wu, L H; Wu, N; Wu, S X; Wu, W; Wu, Z; Xia, L G; Xiao, Z J; Xie, Y G; Xiu, Q L; Xu, G F; Xu, G M; Xu, H; Xu, Q J; Xu, X P; Xu, Z R; Xue, F; Xue, Z; Yan, L; Yan, W B; Yan, Y H; Yang, H X; Yang, Y; Yang, Y X; Ye, H; Ye, M; Ye, M H; Yu, B X; Yu, C X; Yu, J S; Yu, S P; Yuan, C Z; Yuan, W L; Yuan, Y; Zafar, A A; Zallo, A; Zeng, Y; Zhang, B X; Zhang, B Y; Zhang, C C; Zhang, D H; Zhang, H H; Zhang, H Y; Zhang, J; Zhang, J Q; Zhang, J W; Zhang, J Y; Zhang, J Z; Zhang, S H; Zhang, T R; Zhang, X J; Zhang, X Y; Zhang, Y; Zhang, Y H; Zhang, Y S; Zhang, Z P; Zhang, Z Y; Zhao, G; Zhao, H S; Zhao, J W; Zhao, K X; Zhao, Lei; Zhao, Ling; Zhao, M G; Zhao, Q; Zhao, S J; Zhao, T C; Zhao, X H; Zhao, Y B; Zhao, Z G; Zhemchugov, A; Zheng, B; Zheng, J P; Zheng, Y H; Zheng, Z P; Zhong, B; Zhong, J; Zhou, L; Zhou, X K; Zhou, X R; Zhu, C; Zhu, K; Zhu, K J; Zhu, S H; Zhu, X L; Zhu, X W; Zhu, Y C; Zhu, Y M; Zhu, Y S; Zhu, Z A; Zhuang, J; Zou, B S; Zou, J H; Zuo, J X

    2012-01-01

    Using a sample of $(225.2\\pm 2.8)\\times 10^6$ $J/\\psi$ events collected with the BESIII detector, we present results of a study of $J/\\psi\\rightarrow \\gamma\\Lambda\\bar{\\Lambda}$ and report the first observation of the isospin violating decay $J/\\psi\\rightarrow\\Lambda\\bar{\\Sigma}^{0}+c.c.$, in which $\\bar{\\Sigma}^{0}$ decays to $\\gamma \\bar{\\Lambda}$. The measured branching fractions are $\\mathcal{B}(J/\\psi\\rightarrow\\bar{\\Lambda}\\Sigma^{0}$) = $(1.46\\pm0.11\\pm0.12) \\times10^{-5}$ and $\\mathcal{B}(J/\\psi\\rightarrow\\Lambda\\bar{\\Sigma^{0}}$) = $(1.37\\pm0.12\\pm0.11) \\times10^{-5}$. We search for $\\Lambda(1520) \\rightarrow \\gamma \\Lambda$ decay, and find no evident signal, and an upper limit for the product branching fraction $\\mathcal{B}(J/\\psi\\rightarrow\\Lambda\\bar{\\Lambda}(1520)+c.c.)\\times \\mathcal{B}(\\Lambda(1520)\\rightarrow\\gamma\\Lambda)<4.1 \\times10^{-6}$ is set at the 90% confidence level. We also report the observation of $\\eta_{c}\\rightarrow\\Lambda\\bar{\\Lambda}$ in $J/\\psi \\rightarrow \\gamma \\eta_{c}$...

  4. NCBI nr-aa BLAST: CBRC-FCAT-01-1101 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-FCAT-01-1101 ref|NP_001001532.1| chemokine (C-C motif) receptor 7 [Sus scrofa]... dbj|BAC57561.1| chemokine receptor 7 [Sus scrofa] dbj|BAC57929.1| chemokine receptor 7 [Sus scrofa] dbj|BAD...06309.1| chemokine (C-C motif) receptor 7 [Sus scrofa] NP_001001532.1 1e-145 94% ...

  5. NCBI nr-aa BLAST: CBRC-DNOV-01-2689 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-DNOV-01-2689 ref|NP_001001532.1| chemokine (C-C motif) receptor 7 [Sus scrofa]... dbj|BAC57561.1| chemokine receptor 7 [Sus scrofa] dbj|BAC57929.1| chemokine receptor 7 [Sus scrofa] dbj|BAD...06309.1| chemokine (C-C motif) receptor 7 [Sus scrofa] NP_001001532.1 4e-76 89% ...

  6. NCBI nr-aa BLAST: CBRC-ETEL-01-1529 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-ETEL-01-1529 ref|NP_001001532.1| chemokine (C-C motif) receptor 7 [Sus scrofa]... dbj|BAC57561.1| chemokine receptor 7 [Sus scrofa] dbj|BAC57929.1| chemokine receptor 7 [Sus scrofa] dbj|BAD...06309.1| chemokine (C-C motif) receptor 7 [Sus scrofa] NP_001001532.1 0.0 89% ...

  7. NCBI nr-aa BLAST: CBRC-RMAC-16-0027 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-RMAC-16-0027 ref|NP_001001532.1| chemokine (C-C motif) receptor 7 [Sus scrofa]... dbj|BAC57561.1| chemokine receptor 7 [Sus scrofa] dbj|BAC57929.1| chemokine receptor 7 [Sus scrofa] dbj|BAD...06309.1| chemokine (C-C motif) receptor 7 [Sus scrofa] NP_001001532.1 0.0 92% ...

  8. Sequential dynamics in the motif of excitatory coupled elements

    Science.gov (United States)

    Korotkov, Alexander G.; Kazakov, Alexey O.; Osipov, Grigory V.

    2015-11-01

    In this article a new model of motif (small ensemble) of neuron-like elements is proposed. It is built with the use of the generalized Lotka-Volterra model with excitatory couplings. The main motivation for this work comes from the problems of neuroscience where excitatory couplings are proved to be the predominant type of interaction between neurons of the brain. In this paper it is shown that there are two modes depending on the type of coupling between the elements: the mode with a stable heteroclinic cycle and the mode with a stable limit cycle. Our second goal is to examine the chaotic dynamics of the generalized three-dimensional Lotka-Volterra model.

  9. Study on online community user motif using web usage mining

    Science.gov (United States)

    Alphy, Meera; Sharma, Ajay

    2016-04-01

    The Web usage mining is the application of data mining, which is used to extract useful information from the online community. The World Wide Web contains at least 4.73 billion pages according to Indexed Web and it contains at least 228.52 million pages according Dutch Indexed web on 6th august 2015, Thursday. It’s difficult to get needed data from these billions of web pages in World Wide Web. Here is the importance of web usage mining. Personalizing the search engine helps the web user to identify the most used data in an easy way. It reduces the time consumption; automatic site search and automatic restore the useful sites. This study represents the old techniques to latest techniques used in pattern discovery and analysis in web usage mining from 1996 to 2015. Analyzing user motif helps in the improvement of business, e-commerce, personalisation and improvement of websites.

  10. Sulfur-induced structural motifs on copper and gold surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Walen, Holly [Iowa State Univ., Ames, IA (United States)

    2016-01-01

    The interaction of sulfur with copper and gold surfaces plays a fundamental role in important phenomena that include coarsening of surface nanostructures, and self-assembly of alkanethiols. Here, we identify and analyze unique sulfur-induced structural motifs observed on the low-index surfaces of these two metals. We seek out these structures in an effort to better understand the fundamental interactions between these metals and sulfur that lends to the stability and favorability of metal-sulfur complexes vs. chemisorbed atomic sulfur. The experimental observations presented here—made under identical conditions—together with extensive DFT analyses, allow comparisons and insights into factors that favor the existence of metal-sulfur complexes, vs. chemisorbed atomic sulfur, on metal terraces. We believe this data will be instrumental in better understanding the complex phenomena occurring between the surfaces of coinage metals and sulfur.

  11. The sword motif 'n Matthew 10:34

    Directory of Open Access Journals (Sweden)

    David C. Sim

    2000-01-01

    Full Text Available 'n Mathew 10:34 Jesus uters a very dificult saying. He claims that he has not come to bring peace, but a sword. The form of this saying does not trace back to the historical Jesus; it is the product of Matthew's redaction of a Q passage which is found 'n a more original form 'n Luke 12:51. What did the evangelist mean when he wrote that Jesus brought a sword? 'n the Hebrew scriptures the sword was acommon symbol for the judgement and punishment of God, and 'n later times it represented a number of themes associated with the eschaton. It is argued 'n this study that Mathew, who was fully immersed 'n the apocalyptic-eschatological traditions of his day, probably used the sword motif 'n Matthew 10:34 to symbolise anumber of important eschatological events.

  12. Topological defect motifs in two-dimensional Coulomb clusters

    CERN Document Server

    Radzvilavičius, A; 10.1088/0953-8984/23/38/385301

    2012-01-01

    The most energetically favourable arrangement of low-density electrons in an infinite two-dimensional plane is the ordered triangular Wigner lattice. However, in most instances of contemporary interest one deals instead with finite clusters of strongly interacting particles localized in potential traps, for example, in complex plasmas. In the current contribution we study distribution of topological defects in two-dimensional Coulomb clusters with parabolic lateral confinement. The minima hopping algorithm based on molecular dynamics is used to efficiently locate the ground- and low-energy metastable states, and their structure is analyzed by means of the Delaunay triangulation. The size, structure and distribution of geometry-induced lattice imperfections strongly depends on the system size and the energetic state. Besides isolated disclinations and dislocations, classification of defect motifs includes defect compounds --- grain boundaries, rosette defects, vacancies and interstitial particles. Proliferatio...

  13. Bacteria-mimicking nanoparticle surface functionalization with targeting motifs

    Science.gov (United States)

    Lai, Mei-Hsiu; Clay, Nicholas E.; Kim, Dong Hyun; Kong, Hyunjoon

    2015-04-01

    In recent years, surface modification of nanocarriers with targeting motifs has been explored to modulate delivery of various diagnostic, sensing and therapeutic molecular cargo to desired sites of interest in in vitro bioengineering platforms and in vivo pathologic tissue. However, most surface functionalization approaches are often plagued by complex chemical modifications and effortful purifications. To resolve such challenges, this study demonstrates a unique method to immobilize antibodies that can act as targeting motifs on the surfaces of nanocarriers, inspired by a process that bacteria use for immobilization of the host's antibodies. We hypothesized that alkylated Staphylococcus aureus protein A (SpA) would self-assemble with micelles and subsequently induce stable coupling of antibodies to the micelles. We examined this hypothesis by using poly(2-hydroxyethyl-co-octadecyl aspartamide) (PHEA-g-C18) as a model polymer to form micelles. The self-assembly between the micelles and alkylated SpA became more thermodynamically favorable by increasing the degree of substitution of octadecyl chains to PHEA-g-C18, due to a positive entropy change. Lastly, the mixing of SpA-PA-coupled micelles with antibodies resulted in the coating of micelles with antibodies, as confirmed with a fluorescence resonance energy transfer (FRET) assay. The micelles coated with antibodies to VCAM-1 or integrin αv displayed a higher binding affinity to substrates coated with VCAM-1 and integrin αvβ3, respectively, than other controls, as evaluated with surface plasmon resonance (SPR) spectroscopy and a circulation-simulating flow chamber. We envisage that this bacteria-inspired protein immobilization approach will be useful to improve the quality of targeted delivery of nanoparticles, and can be extended to modify the surface of a wide array of nanocarriers.In recent years, surface modification of nanocarriers with targeting motifs has been explored to modulate delivery of various

  14. ABP: a novel AMPA receptor binding protein.

    Science.gov (United States)

    Srivastava, S; Ziff, E B

    1999-04-30

    We review the cloning of a novel AMPA receptor binding protein (ABP) that interacts with GluR2/3 and is homologous to GRIP. ABP is enriched in the PSD with GluR2 and is localized to the PSD by EM. ABP binds GluR2 via the C-terminal VXI motif through a Class I PDZ interaction. ABP and GRIP can also homo- and heteromultimerize. Thus, ABP and GRIP may be involved in AMPA receptor regulation and localization, by linking it to other cytoskeletal or signaling molecules. We suggest that the ABP/GRIP and PSD-95 families form distinct scaffolds that anchor, respectively, AMPA and NMDA receptors. We are currently investigating proteins that bind ABP and that may regulate the AMPA receptor.

  15. Polyproline and triple helix motifs in host-pathogen recognition.

    Science.gov (United States)

    Berisio, Rita; Vitagliano, Luigi

    2012-12-01

    Secondary structure elements often mediate protein-protein interactions. Despite their low abundance in folded proteins, polyproline II (PPII) and its variant, the triple helix, are frequently involved in protein-protein interactions, likely due to their peculiar propensity to be solvent-exposed. We here review the role of PPII and triple helix in mediating hostpathogen interactions, with a particular emphasis to the structural aspects of these processes. After a brief description of the basic structural features of these elements, examples of host-pathogen interactions involving these motifs are illustrated. Literature data suggest that the role played by PPII motif in these processes is twofold. Indeed, PPII regions may directly mediate interactions between proteins of the host and the pathogen. Alternatively, PPII may act as structural spacers needed for the correct positioning of the elements needed for adhesion and infectivity. Recent investigations have highlighted that collagen triple helix is also a common target for bacterial adhesins. Although structural data on complexes between adhesins and collagen models are rather limited, experimental and theoretical studies have unveiled some interesting clues of the recognition process. Interestingly, very recent data show that not only is the triple helix used by pathogens as a target in the host-pathogen interaction but it may also act as a bait in these processes since bacterial proteins containing triple helix regions have been shown to interact with host proteins. As both PPII and triple helix expose several main chain non-satisfied hydrogen bond acceptors and donors, both elements are highly solvated. The preservation of the solvation state of both PPII and triple helix upon protein-protein interaction is an emerging aspect that will be here thoroughly discussed.

  16. Nonstructural 5A Protein of Hepatitis C Virus Interferes with Toll-Like Receptor Signaling and Suppresses the Interferon Response in Mouse Liver

    Science.gov (United States)

    Okushin, Kazuya; Enooku, Kenichiro; Fujinaga, Hidetaka; Moriya, Kyoji; Yotsuyanagi, Hiroshi; Aizaki, Hideki; Suzuki, Tetsuro; Matsuura, Yoshiharu; Koike, Kazuhiko

    2017-01-01

    The hepatitis C virus nonstructural protein NS5A is involved in resistance to the host immune response, as well as the viral lifecycle such as replication and maturation. Here, we established transgenic mice expressing NS5A protein in the liver and examined innate immune responses against lipopolysaccharide (LPS) in vivo. Intrahepatic gene expression levels of cytokines such as interleukin-6, tumor necrosis factor-α, and interferon-γ were significantly suppressed after LPS injection in the transgenic mouse liver. Induction of the C-C motif chemokine ligand 2, 4, and 5 was also suppressed. Phosphorylation of the signal transducer and activator of transcription 3, which is activated by cytokines, was also reduced, and expression levels of interferon-stimulated genes, 2’-5’ oligoadenylate synthase, interferon-inducible double-stranded RNA-activated protein kinase, and myxovirus resistance 1 were similarly suppressed. Since LPS binds to toll-like receptor 4 and stimulates the downstream pathway leading to induction of these genes, we examined the extracellular signal-regulated kinase and IκB-α. The phosphorylation levels of these molecules were reduced in transgenic mouse liver, indicating that the pathway upstream of the molecules was disrupted by NS5A. Further analyses revealed that the interaction between interleukin-1 receptor-associated kinase-1 and tumor necrosis factor receptor associated factor-6 was dispersed in transgenic mice, suggesting that NS5A may interfere with this interaction via myeloid differentiation primary response gene 88, which was shown to interact with NS5A. Since the gut microbiota, a source of LPS, is known to be associated with pathological conditions in liver diseases, our results suggest the involvement of NS5A in the pathogenesis of HCV infected-liver via the suppression of innate immunity. PMID:28107512

  17. Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins

    Directory of Open Access Journals (Sweden)

    Vassilev Boris

    2010-04-01

    Full Text Available Abstract Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94% appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1 a dimer interface motif found in voltage-gated chloride channels, (2 a proton transfer motif found in heme-copper oxidases, and (3 a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b. Conclusions Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.

  18. Assembly of supramolecular DNA complexes containing both G-quadruplexes and i-motifs by enhancing the G-repeat-bearing capacity of i-motifs

    Science.gov (United States)

    Cao, Yanwei; Gao, Shang; Yan, Yuting; Bruist, Michael F.; Wang, Bing; Guo, Xinhua

    2017-01-01

    The single-step assembly of supramolecular complexes containing both i-motifs and G-quadruplexes (G4s) is demonstrated. This can be achieved because the formation of four-stranded i-motifs appears to be little affected by certain terminal residues: a five-cytosine tetrameric i-motif can bear ten-base flanking residues. However, things become complex when different lengths of guanine-repeats are added at the 3′ or 5′ ends of the cytosine-repeats. Here, a series of oligomers d(XGiXC5X) and d(XC5XGiX) (X = A, T or none; i < 5) are designed to study the impact of G-repeats on the formation of tetrameric i-motifs. Our data demonstrate that tetramolecular i-motif structure can tolerate specific flanking G-repeats. Assemblies of these oligonucleotides are polymorphic, but may be controlled by solution pH and counter ion species. Importantly, we find that the sequences d(TGiAC5) can form the tetrameric i-motif in large quantities. This leads to the design of two oligonucleotides d(TG4AC7) and d(TGBrGGBrGAC7) that self-assemble to form quadruplex supramolecules under certain conditions. d(TG4AC7) forms supramolecules under acidic conditions in the presence of K+ that are mainly V-shaped or ring-like containing parallel G4s and antiparallel i-motifs. d(TGBrGGBrGAC7) forms long linear quadruplex wires under acidic conditions in the presence of Na+ that consist of both antiparallel G4s and i-motifs. PMID:27899568

  19. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun

    2015-09-27

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  20. Mechanical and Chemical Characterization of a TiC/C System Synthesized Using a Focus Plasma Arc.

    Directory of Open Access Journals (Sweden)

    Reza Mahmoodian

    Full Text Available Titanium carbide-graphite (TiC/C composite was successfully synthesized from Ti and C starting elemental powders using self-propagating high-temperature synthesis technique in an ultra-high plasma inert medium in a single stage. The TiC was exposed to a high-temperature inert medium to allow recrystallization. The product was then characterized using field emission scanning electron microscopy (FESEM coupled with energy dispersive X-ray analysis (EDX, X-ray diffraction (XRD, Rietveld refinement, nanoindentation, and micro-hardness to determine the product's properties. The recorded micro-hardness of the product was 3660 HV, which is a 14% enhancement and makes is comparable to TiC materials.